[gmx-users] gmx trjconv -force option doesn't seem to work.

Hello! I have a question about gmx trjconv -force option because it seems to work at all. I'm using GROMACS-5.1.5 version and I want to extract forces using gmx trjconv command. So I tried. gmx trjconv -f alad.trr -s alad.tpr -n alad.ndx -novel -force yes

[gmx-users] cudaFuncGetAttributes failed: out of memory

Hello, I have encountered a weird problem. I've been using GROMACS with GPU on a server and always performance good. However when I just reran a job today and suddenly got this error: Command line: gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3　 Back Off! I just backed up

[gmx-users] How to deal with unexpected reactions in umbrella sampling?

Dear Colleagues, I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However, as the reaction coordinate exceeds a certain value, an unexpected reaction, which is obviously unreasonable, often occurs during the umbrella sampling. So, how to deal with such problem? The only

Re: [gmx-users] How to cap a single residue in gromacs

Hi, Without saying about the physical meaning of your model because I don't know what you are doing. About technical point, I used your PHE coordinate and using pymol to cap with ACE, NME as you said then execute pdb2gmx using amber99sb forcefield in gromacs, it works well. What is the error that

Re: [gmx-users] GPU considerations for GROMACS

We recommend Intel Xeon if possible. You can see how we set up our GROMACS optimized workstations at https://www.exxactcorp.com/GROMACS-Certified-GPU-Systems If Xeon is not an option, at the very least use a high-end i7 or i9 9th/10th gen. With Memory the system should typically have 64GB to

Re: [gmx-users] GPU considerations for GROMACS

Hi, A CPU:GPU ratio of 4:1 is fairly well balanced these days (depending on the quality of the hardware), so you should expect to roughly double your throughput adding a second GPU to your current system. However, that doesn't mean your single simulation performance will double - it's a lot more

[gmx-users] Converting Charmm to gmx format using cgenff

Dear gmx users, I am trying to generate topology for small ligands using cgenff . I will like to confirm if the Charmm to gmx script available on the Mackerell website is compatible with all versions of charmm forcefield or can only be used with Charm36 forcefield. P.S. I have tried it with

Re: [gmx-users] Selective RMSD calculation

Hi, You can calculate the rmsd by passing the index file of the ligand... gmx rms -h On Wed 19 Feb, 2020, 7:41 PM Peter Mawanga, wrote: > Hello everyone > > After fitting the protein-ligand system to the starting conformation, I > would like to extract the RMSD information for the ligand

[gmx-users] Selective RMSD calculation

Hello everyone After fitting the protein-ligand system to the starting conformation, I would like to extract the RMSD information for the ligand only but cannot find such an option for a selective output. Please let me know if this can be achieved with the gmx tool, I couldn't find such an

Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa)

Thank you, Alessandra, for your reply. I have tried TER in the PDB file but it doesn't work. It requires an N and C terminal for amino acid residue. I have prepared residue in avogadros and used these coordinates. ATOM 1 N PHE A 1 0.000 0.000 0.000 1.00 0.00 N1+ ATOM 2

Re: [gmx-users] Increase Graphene sheet size

Hi Alessandra, Many thanks again for your help :) That sounds great. I can simulate a box with the desired dimensions. I repeated the graphene sheet using genconf into dimensions greater the desired dimensions and then I created a box with the desired dimensions and I solvate it to visualize

Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3

Hi, On Wed, Feb 19, 2020 at 11:06 AM Robert Cordina wrote: > Dear Alessandra, > > Many thanks for your reply. > Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that > "In the NERD force field, atoms/sites within a molecule that do not > interact by any other intramolecular

Re: [gmx-users] Increase Graphene sheet size

HI, On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal wrote: > Many thanks Alessandra for your reply :) > > gmx solvate will add water around my graphene sheet but will not increase > the graphene sheet itself. Please correct me if I am wrong. > > Yes/No, gmx solvate is normally used to add

Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3

Dear Alessandra, Many thanks for your reply. Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that "In the NERD force field, atoms/sites within a molecule that do not interact by any other intramolecular potential are also allowed to interact though the Lennard-Jones

Re: [gmx-users] Increase Graphene sheet size

Many thanks Alessandra for your reply :) gmx solvate will add water around my graphene sheet but will not increase the graphene sheet itself. Please correct me if I am wrong. I already simulated the graphene sheet but I need to increase its dimension to a certain dimensions. any Ideas how to do

Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3

HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure

Re: [gmx-users] How to cap a single residue in gromacs

Hi On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani wrote: > Dear Gromacs users > I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand > when I run pdb2gmx it gives me error:- > Fatal error: > In the chosen force field there is no residue type for 'PHE' as a > standalone >

Re: [gmx-users] Tabulated potentials

Hi, On Tue, Feb 18, 2020 at 12:12 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > So I am using Iterative Boltzmann Inversion to get the CG potentials for a > cellobiose-water solution. During the first step of the simulation by > gromacs, I get the error, which I think it might