Re: [gmx-users] Force Field for Small Molecule

I think you should recalculate charged of atoms of that molecule, the other properties can used from GAFF URL: https://qvu.netlify.com/#/ On Wed, Jun 20, 2018 at 3:36 AM Wahl, David M wrote: > Hello, > > > I am working on a molecular dynamics simulation in GROMACS and am curious > as to which

Re: [gmx-users] Force Field for Small Molecule

​I think you should recalculate charged of atoms of that molecule, the other properties can used from GAFF -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Question regarding running Gromacs new graphics card on Centos

Hi everyone, I have been using Gromacs 2016.3 with GPU-acceleration with CUDA on Centos 7 for a year. I am a beginner as a programmer. I was using Nvidia GTX1050, but now I replaced it with Nvidia GTX1070Ti. For sole purpose of running Gromacs with FFTW and CUDA, will it cause a calculation error

[gmx-users] Force Field for Small Molecule

Hello, I am working on a molecular dynamics simulation in GROMACS and am curious as to which force field will be the best to run a simulation on a small organic molecule containing carbon, nitrogen, oxygen and hydrogen. Through some research it seems that the general Amber force field (gaff)

[gmx-users] How to generate multiple diverse trajectories from one checkpoint file

Hi, everyone: I am testing some transition path sampling (TPS) algorithms using GROMACS. For certain type of TPS methods, such as the weighted ensemble method, it requires to restart multiple simulations from a checkpoint and those simulations needs to be stochastic. In other words, the

[gmx-users] GROMACS2016.1 Compiling with ORCA

Hi, I want to compile gromacs 2016.1 with ORCA 4.0.1 and I was going through the file CMakeList.txt and I arrived at the following inputs in line 264[1]. So when I compile GROMACS2016 with ORCA this do I have to call this command somehow? Also looking at [1] I see that "None" is mentioned twice.

Re: [gmx-users] .mdp file for calculating surface tension of water

Den 2018-06-19 kl. 14:52, skrev Rana Ali: Dear expert users It will be of great help if somebody share the .mdp file for calculating the surface tension of water using NVT ensemble Thank in advance Regards Rana Check: http://virtualchemistry.org/ff.php -- David van der Spoel, Ph.D.,

[gmx-users] .mdp file for calculating surface tension of water

Dear expert users It will be of great help if somebody share the .mdp file for calculating the surface tension of water using NVT ensemble Thank in advance Regards Rana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Error running mdrun (v-5.1.4) on a linux cluster.

Thanks Mark for your response. I looked into the PBS script and it does have a line pointing to the PBS workdir. But what you said seems right. Somehow, the execution of the script is not happening correctly. As it turns out, I realized that I was submitting the script within a qlogin session,

Re: [gmx-users] Gromacs tabulated potentials for CG models

Dear All, Please find two more files in the attachment which I forgot to attach in my previous mail in this thread. Regards, Sudip ‌ Sudip Das PhD Student C/o. Prof. S. Balasubramanian Molecular Simulations Lab Chemistry and Physics of Materials Unit (CPMU) Jawaharlal Nehru Centre for

[gmx-users] Gromacs tabulated potentials for CG models

Dear All, I want to use Gromacs to simulate my coarse-grain model. Our group developed the coarse-grain parameters for the system of interest. The non-bonded parameters are having a different potential form for different pairs. I came across a documentation (

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

Hello Justin, could you specify please a bit more. Following your method, if the simulation has been terminated by crash without producing gro file so to re-initiate it I only need one command: gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append where the last_checkpoint should be

[gmx-users] Error : symtab get_symtab_handle 367 not found

Hi, I am simulating a Martini coarse grained DNA protamine system. I have 1 infinite DNA + 1 protamine. Since while using the martini python script for coarse graining it removes the 2 phosphate atoms of the terminal base pairs, so in order to have the right infinite DNA system, while building

[gmx-users] analysis of angle between two beta sheet of martini protein cg

hi, i want to calculate the angle between the two beeta sheet of a protein.for this reason i have made a index file containing two beeta sheet group.can anyone please suggest me how can i do this. i am using this command gmx gangle -f ../pbc340.xtc/md-340k-0-1 -s ../equilibration.gro -n

[gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section

Dear Gromacs users, I am trying adding Na ions: genion -s ions.tpr -o 1lipidA_solv.g96 -p lipidA_gromacsBien.top -pname NA -np 2 But I get this error: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'lipidA_gromacsBien.top' I have check the .top file and I

Re: [gmx-users] Error running mdrun (v-5.1.4) on a linux cluster.

Hi, You aren't running mdrun_mpi from the working directory in which testfile.tpr is found. Probably you need to set some flag in your submission script to change to the directory from which you submitted Mark On Tue, Jun 19, 2018 at 7:41 AM Abhishek Acharya wrote: > Dear GROMACS users, > > I

Re: [gmx-users] spatial restraints

Thanks Simon, I will try that way Stefano 2018-06-19 4:11 GMT+02:00 Simon Kit Sang Chu : > Hi Stefano, > > You may consider "gmx make_ndx" to make an index file and append a > restraint section (POSRES) at the end of your existing topology to call the > indices. > > I think this is a minimal