I'm doing a PhD in computational drug discovery using ML/CNN-based QSAR models to screen large libraries of natural products. I also employ docking and molecular dynamics simulations. I recently learned that CompChem and Cheminformatics are different fields so I'm confused which discipline and which specialty to put in my final draft. Thanks in advance.

Dear all,

I am relatively new to orca, but have been reading non-stop for the past few days so I am slowly getting accustomed to it. My purpose for using orca is to simulate an IR spectrum and to compare it to an experimentally observed one. To begin, I simply wanted to simulate the spectrum of sodium carbonate in order to assess the accuracy of Orca and see if I grasped the tool correctly.

After having tried this seemingly simple endeavor with various different basis sets, scf convergence tightnesses and functionals, I have yet to successfully replicate the experimentally observed sodium carbonate spectrum. From my understanding, this is because orca simulates the spectrum of molecules in the gaseous phase, whereas i am working with a crystalline solid (although this does not appear to be an issue for other researchers). I therefore suppose that I must run the geometry and frequency optimizations on a dimer/trimer/x-mer of crystalline sodium carbonate, but am unsure as to how to proceed (a .cif of Na2CO3 can be imported directly from the Avogadro "File - import" drop down menu if ever).

How does one go about simulating frequencies for repeating crystalline units? Does this require me to use the MOL-CRYSTAL-QMMM calculation? Do I need to freeze certain parts of the crystal in order to facilitate converging? What about charge and multiplicity in the case of repeating crystalline structures? What kind of computation time am I looking at here, considering a standard personal computer?

Thanks in advance for your help

​

​

I am working on some DFT calculations using orca and avagadro. I build just H-F in avagadro. Then made an input file using the following code in the preview of advanced parameters:

! Largeprint B3LYP OPT cc-pvdz def2/J tight SCF %output print[p_mos] true end

Then there is the xyz coordinates.

When I generate this as a .inp file I go to terminal and type

orca filname.inp > filename.out

The calculation then runs. The issue is that after the calculation is done the text file is missing the homo Lumo calculations and only SCF energy and geometries!

Help

Hi everyone. I am trying to build a crystal lattice from the unit cell information, given here in https://www.ccdc.cam.ac.uk/structures/search?id=doi:10.5517/ccvfcxj&sid=DataCite Is there any program or tools available which can do that? For more info, I just want to build like a box which incorporate the unit cell information for running further molecular dynamics simulation. Thanks.

I am a newbie using VASP, currently I am trying to calculate the formation energy per atom and pre bandgap using dft with VSAP.

I wrote script for calculating the bandgap

from  import read
from ase.calculators.vasp
import Vasp from ase.optimize
import BFGS
import numpy as np import os

os.environ['VASP_PP_PATH'] = '/scratch'

# Load the structure from a CIF file
structure = read('mp-1218989.cif')

# Set up VASP calculator for relaxation
calc_relax = Vasp(xc='PBE', # Exchange-correlation 
                  functional encut=400, # Plane-wave cutoff 
                  kpts=(3, 3, 3), # k-point grid for relaxation 
                  ibrion=2, # Ion relaxation: CG algorithm 
                  nsw=50, # Number of steps for ionic relaxation 
                  ismear=0, # Gaussian smearing 
                  sigma=0.05, # Width of smearing in eV 
                  lreal='Auto', # Use real-space projection for GPU acceleration
                  command='mpirun -np 1 vasp_gpu') # VASP run command

# Attach the calculator to the structure for relaxation
structure.set_calculator(calc_relax)

# Optimize the structure
opt = BFGS(structure) opt.run(fmax=0.01)

# Now setting up the NSCF calculation for band structure
calc_nscf = Vasp(xc='PBE', # Exchange-correlation functional 
                  encut=400, # Plane-wave cutoff 
                  kpts=(11, 11, 11), # denser k-point mesh for band structure 
                  ismear=0, # Gaussian smearing (must use ISMEAR < -1 or 0) 
                  sigma=0.05, 
                  ibrion=-1, # No ionic relaxation 
                  nsw=0, # No ionic steps 
                  icharg=11, # Non-self-consistent field run 
                  command='mpirun -np 1 vasp_gpu')

# Attach the non-self-consistent calculator
structure.set_calculator(calc_nscf)

# Calculate the electronic structure (no need to run optimize)
structure.calc.calculate(structure)

# Extract eigenvalues
eigenvalues = structure.calc.get_eigenvalues(kpt=0, spin=0) # For the first k-point and spin

# Calculate bandgap
occupied = np.max(eigenvalues[eigenvalues < 0]) 
unoccupied = np.min(eigenvalues[eigenvalues > 0]) 
bandgap = unoccupied - occupied

print('Bandgap (PBE):', bandgap, 'eV')ase.io

I still didn't figured out how to calculate the formation energy

their is some problems I am currently facing

1. the above code is not utilising the gpu properly
2. I am planning to perfom this on 100 molecules so any better method ?

please help if any one knows simple method to automate the calculation of the properties using vasp

Just out of curiosity, why is the string "GradGradGrad..." used to delimit the output from the Berny optimization procedure in calculations performed using Gaussian? Does the string have any meaning or is it just a jumble of nonsense?

How to do partial charge calculation of a molecules by writing program by python or perl? Is there any source or book to help me? I want to use that materials for MD simulation.

What is the difference between computational chemistry and cheminformatics? Are they related?

I'm teaching some new folks in my lab and getting them set up to do work on their own. We use Gaussian for calculations, but only have a single computer with Gaussview.

I primarily use PCs and have some ways to get work done without GV, but I don't really use Macs and unfortunately two of the people I'm training use them. I know Avogadro should work on Macs but I find parts of the output file manipulation difficult as it is, so I'd like to hear about alternatives. We are limited to free/low cost software, because grad students.

Any recommendations for FTP clients, SSH programs, and robust text editors (ideally that can handle some regular expressions) would also be helpful.

If you have any suggestions for GUIs for building molecules, generating input files, and reading output files, that would be truly amazing.

So I tried installing these packages in Anaconda Prompt on Windows 11 as instructed by my lecturer, and received the following error: 

(base) C:\>conda install -c conda-forge nglview ipywidgets scipy pandas jupyterlab jupyterlab_widgets nodejs mdanalysis gromacs

Channels:
- conda-forge
- defaults
Platform: win-64
Collecting package metadata (repodata.json): done
Solving environment: failed
 
PackagesNotFoundError: The following packages are not available from current channels:
 
  - gromacs
 
Current channels:
 
  - defaults
  - https://conda.anaconda.org/conda-forge

To search for alternate channels that may provide the conda package you're
looking for, navigate to https://anaconda.org and use the search bar at the top of the page.

Running

conda install conda-forge::gromacs

as well as

conda install bioconda::gromacs

produced the same result.

What's wrong? Any assistance will be much appreciated.

I want to calculate the FMO overlap of two fragments of a TS.

Any idea with which software I can do it?

Hi everyone!!

Please don’t laugh but I am extremely (EXTREMELY) new to MD simulations and was needing some guidance.

How long does it take to get familiar with MD simulations. My project involves studying the interaction between 2 molecules and how temperature and other properties change of the system when the two molecules are interacting. I was planning on using GROMACs but is there a better (easier) software to use?

How do you even get started??

Hello, everyone!

I'm trying to run Gaussian 16 through WSL (Windows Subsystem for Linux), but my CPU usage is not matching what I describe in the input.

This is my input!

​

The use of my CPU while calculating

​

I don't know if it's necessary, but I have MPI installed in WSL.

​

Is it possible to use all my CPU cores in Gaussian calculations running in WSL?

By the way, my CPU has six physical cores and twelve logical cores (threads).

Thanks in advance!!

​

Hello! My name is Gauri and I am currently nearing the end of my 11th grade. We have this research project called an Extended Essay and I have chosen to do it around the use of CRISPR-cas9 as a therapy for sickle cell anaemia. Ironically, this "essay" is actually to be an experiment and hence if I want to proceed I would need to use computational models.

According to research, a custom adenine base editor, namely ABE8e-NRCH has been used to convert the pathogenic allele to a makassar non pathogenic variant. Is there any platform that can allow me to test out this modified CRISPR-cas9 online for free? And how exactly do I go about learning the process?

Lastly, I also needed sort of incremental IV that changes the DV and Im not sure what it would be with this kind of data?

Thanking you for your time and consideration.

Hi all, can someone familiar with exciting code please have a look at my post on the forum? I'm kind of desperate rn. TLDR: density of states comes out to 0 for certain energy values and this should not be possible.

Hey, I'm one of the cofounders of Leash Biosciences, a seed-stage biotech/techbio startup in Salt Lake City. We noticed that there is some appetite for novel computational methods but not a lot of public data to try them on, and so we released some to shore up the gap a little.

The Big Encoded Library for Chemical Assessment (BELKA) challenge asks contestants to predict whether small molecules might bind to one of three protein targets, and we provide ~100M physical measurements as training examples (SMILES and a binary "bind or not" label) for each of those targets. Some members of this community might enjoy the contest - please compete! There are cash prizes ($50k total) and we are excited for folks to play with the data.

When the competition is over (July 8), we'll be releasing the raw data (replicates, etc.) publicly, which amounts to some 3.6B physical measurements between small molecules and protein targets. Blog post on the whole endeavor here. Hope you guys have fun!

Hello, it's my first time doing DLPNO-CCSD(T) single point calculations.

I did a run (cc-PVQZ) on a 32 and 62 atom system that ran for ~2 and ~6.5 hrs respectively (85 cores), I have a few questions:

1. Is the method supposed to be very very blackbox? I am mostly trained in DFT. Is CCSD(T) meant to be "easier" to run than DFT (as far as single points are concerned)? I don't have to find a functional!

2. I thought DLPNO scales linearly? Why did my 62 atom system ran for 3x the length of the 32 atom one? (The 62 atom system is a dimeric form of the 32 atoms)

3. Can I use CCSD(T) energy and use a DFT zero point correction for thermochemical quantities, or does it have to be purely derived from DFT?

4. Why are my "garbage" DFT energies i.e. 6-31G/B3LYP/D4 performing better than the more expensive ones, i.e. def2-SVP/PBE0-DH/D4 if I compare with the CCSD(T) energy?

Hi,

I'm a master’s student in computational chemistry and machine learning. I originally studied materials engineering but switched to comp chem because I'm more interested in software and coding, and I want to keep my options open for tech jobs if I can't find work in comp chem.

I've been diving into quantum chemistry, molecular dynamics, and electronic structure methods, but I haven't had much time to beef up my technical and computing skills. With my master's ending soon, I want to make sure I have good job options.

For those already working in tech or related fields like chemistry research or pharma—even if it's not directly related to chemistry—what are the key practices for getting hired? I don’t want to just avoid spaghetti code; I’m looking for specific advice. What should I learn? How should I go about it? What Python libraries do you use most? And how can I combine skills like data pipelines and machine learning to be more attractive to companies? I just want to build a solid skill set that will help me get hired.

Thanks for any tips you can share!

Hi everyone, happy Friday!

I am looking to build a high-throughput automated DFT workflow. I have come across pymatgen and AiIDA. Has anyone got any experience using these softwares/building a HT automated DFT workflow and could advise whether it is worth starting from scratch?

Thanks!

Greetings,

I'm currently working on implementing my own Hartree-Fock (and later DFT) code.
I was wondering if there is a database for the solutions of the overlap-, Fock-matrix, etc. Integrals for the different basis sets (e. g. STO-3G, STO-6G, 6-311G)?

Thanks in advance!

Hi all,

I just realized the way I made my VN slab seems to induce magnetization in the structure. This follows this author's work,. (Check VN electronic structure not symmetric). This puts a wrench in my adsorption process because after optimizing the unit cell from the databases, I would need to turn on magnetization for the slab structure with virtually no initial guess for QE's starting magnetization for each atom. Probably test it 2-3 times to converge to the right total_mag and then use that for the combined structure for adsorption. This PBC PW stuff seems such a hassle now.

Any one dealt with a situation like this? Is my updated process sound?

Thank you

Hey everyone,

I’m diving into running equilibration and dynamics simulations with Amber, and I could use some guidance on the necessary commands. Specifically, I’m curious about the differences between crd, rst7, and rst file formats.

Could someone please outline all the commands required to launch both equilibration and dynamics simulations in Amber? Additionally, what differentiates crd, rst7, and rst file formats in this context?

I run equilibration with pmemd.cuda and I used -0 -i eq.in -p XX.prmtop -c previous_file.crd -r eq.crd -x eq.mdcrd -o eq.ou -inf eq.log -x eq.nc

Whereas for the md I used -O -i md.in -o md.out -p XX.prmtop -c eq.crd -r md.crd -x md.mdcrd -inf md.log

How can I restart a crashed dynamics simulation? Should I use the crd file, or should I have an rst/rst7 file? What modifications should I make to the input to achieve this?

Hi, i encountered the Problem that the wavefunction won't converge. I have optimized geometry, and used the coordinates for SP calculations using the same functional (r2SCAN-3c). For a neutral or the Anion (Charge 0/-1 and multiplicity 1/2) the sp converged, however for the cation the calculation won't converge. I've tried to decrease from VeryTightSCF to TightDCF and increased MaxIter to 1000, won't help tho.

Input File:

%maxcore 1000 %pal nprocs 20 end %scf MaxIter 1000 end
! r2SCAN-3c
! CPCM(DMSO) 
! TightSCF
*xyz 1 2 O -1.03597521905662 0.51013999011968 3.45273402387167 C -0.34723835267862 1.39987659916967 2.97202151514077 N 1.053021053 ...
*

Last few lines from Outputfile:

  ---------------------------------
          TRAH Step control 
 ---------------------------------
  predicted energy change = -0.000003
  actual energy  change   = 0.000000
  energy change ratio     = -0.165674
  old trust radius        = 0.000000
  new trust radius        = 0.000000
  reject step?            =  1
  974       -709.261359355538     1.871961e-03                     0.000 (TRAH MAcro)  Yes
  975       -709.261359355538     1.445107e-03                     0.000 (TRAH MAcro)   No
WARNING : small    HOMO - LUMO gap : (op =  beta) 0.005933
  975     dE    -2.411033e-06     1.380047e-03    -1.3171e+00      0.001 (TRAH MIcro)
  975     dE    -2.529200e-06     1.057892e-04    -1.3459e+00      0.001 (TRAH MIcro)

               *****************************************************
               *                      ERROR                        *
               *        SCF NOT CONVERGED AFTER 1759 CYCLES         *
               *****************************************************


---------------
SCF CONVERGENCE
---------------

  Last Energy change         ...    0.0000e+00  Tolerance :   1.0000e-08
  Last Orbital Gradient      ...    1.4451e-03  Tolerance :   1.0000e-05
  Last Orbital Rotation      ...    9.3765e-04

             **** DENSITY CaLa-N-1.scfp WAS UPDATED ****
             **** ENERGY FILE WAS UPDATED (CaLa-N-1.en.tmp) ****

     --------------------------------------------------------------------
                                      WARNING
     The wavefunction IS NOT YET CONVERGED! It shows however signs of
     convergence. Therefore the wavefunction will be stored and can be
     used as input for another calculation. 
     DO NOT USE THIS WAVEFUNCTION  FOR ANYHTING ELSE. It is NOT RELIABLE
     --------------------------------------------------------------------

TIMINGS
Total SCF time: 0 days 1 hours 10 min 42 sec
Total time .... 4242.396 sec Sum of individual times .... 4029.426 sec ( 95.0%)
Fock matrix formation .... 2670.466 sec ( 62.9%) Split-RI-J .... 382.376 sec ( 14.3% of F) XC integration .... 2269.011 sec ( 85.0% of F) Basis function eval. .... 54.808 sec ( 2.4% of XC) Density eval. .... 875.164 sec ( 38.6% of XC) XC-Functional eval. .... 30.382 sec ( 1.3% of XC) XC-Potential eval. .... 382.709 sec ( 16.9% of XC) Diagonalization .... 4.021 sec ( 0.1%) Density matrix formation .... 26.476 sec ( 0.6%) Population analysis .... 0.000 sec ( 0.0%) Initial guess .... 0.435 sec ( 0.0%) Orbital Transformation .... 313.057 sec ( 7.4%) Orbital Orthonormalization .... 0.000 sec ( 0.0%) DIIS solution .... 2.194 sec ( 0.1%) Grid generation .... 1.076 sec ( 0.0%)
Maximum memory used throughout the entire SCF-calculation: 89.2 MB
                      DFT DISPERSION CORRECTION                            
                                                                           
                             DFTD4 V2.5                                    
The R2SCAN3C composite method is recognized Using three-body term ABC Active option DFTDOPT ... 5
Starting D4
Dispersion correction -0.012920539
gCP correction 0.015798494
FINAL SINGLE POINT ENERGY -709.258481400326 (Wavefunction not fully converged!)
 ------------------------------------------------------------------------------
                                  ERROR
 This wavefunction IS NOT FULLY CONVERGED! 
 You can't use it for properties or numerical calculations !
 Aborting the run ...
 Please restart calculation (with larger maxiter/different convergence flags)
 ------------------------------------------------------------------------------

EDIT
for people with similar problems:

Use another !similar! file as an initial guess with !MOREAD %moinp "your initial guess", disable TRAH and switch to KDIIS+SOSCF !NoTRAH KDIIS SOSCF

For me this caused the originally "infinite" computing time to reduce to just 1 minute :)

I need to model an instristically disordered protein. I know this this force field will help but I can't seem to find it anywhere online. I only seem to find a gromacs format ff.

Hello all:

I am doing Gromacs MD simulations of protein-ligand and it worked perfectly. However, I do not know what parameters I need to change to perform a protein-only simulation. Does anyone have some parameters for this type of simulation?

Thanks all!!!!

Hey everyone,
I'm currently working with velocity and position data from a molecular dynamics (MD) simulation, and I could use some advice on how to analyze it. Essentially, I have data for a single particle's motion over 1000 time steps, represented as a numpy tensor with shape (1000, 1, 3). Here, 1000 is the number of time steps, 1 is the number of particles, and 3 represents the x, y, or z coordinates.

Now, my professor has asked me to compute the time averages of both <v> and <v^2> and plot them against time. However, I'm a bit confused because <v> and <v^2> are essentially just single numbers in this case.

If I had n number of particles so that my data is (1000, n, 3) then I could average over n and since the equilibrium average, time average should be the same as ensemble average, I could plot them against time.

My code:

output = []

for t in range(1000): # number of steps

vels_data = atom_data[t,:, :] # (1,3) matrix; for n particles this is (n, 3)

v2 = np.mean(np.sum(vels_data**2, axis=1)) # <v^2>

v = np.linalg.norm(np.mean(vels_data, axis=0))

output.append([t, v, v2])

Could anyone advise me on how to computationally compute and plot <v> and <v^2> vs time from this data? I'd greatly appreciate any guidance on the practical implementation, rather than the theoretical aspects.
Thanks in advance for your help!

PS: I believe it is straightforward and I can write my own code. I feel like I am missing something in my understanding.

Amino acids, hydrogen bond distances, in a particular protein
along with other various properties of binding

Hi all, I am trying to restart my geometry optimization job in Gaussian. The job ended for a mundane reason - ran out of allocated time on my university’s computer cluster.

I followed the instructions on the Gaussian FAQ and set # opt = restart. When I ran the job it failed with an ONIOM not found on unit 2 error. I changed the %chk= line to have the explicit path to the .chk file and it returned the same error.

I am absolutely stumped, if anyone has any insight or advice I would greatly appreciate it. Thanks!

Dear Redditors,

I'm relatively new to MD Simulations and have a question. I build a simulation PC with a RTX 4090 to accelerate our simulations. We want to model an RNA with the TIP4P-EW water model and some ions to investigate folding. When I run my simulation I can set the -pme and -bonded flag to GPU but when I want to use the -update flag it fails and complains about --> 'The number of coupled constraints is higher than supported in the GPU LINCS code.' and I get also some complains about virtual sites are not supported.

What would be the solution to this? and are virtual sites and the TIP4P-Ew water model not yet supported by GROMACS 2024.1?