[gmx-users] how to visualize gromacs trajectory

Dear all, I wish to know what is the best way to visualize gromacs trajectory. When I load a gromacs trajectory into VMD, I find some of the water molecules and some part of the protein in the system are streched and the structure become weild and cannot be properly analyzed. I searched google

Re: [gmx-users] How to install gromacs on cpu cluster

Thank you Benson. These are very helpful. Yeping -- From:Benson Muite Sent At:2019 Jul. 1 (Mon.) 20:41 To:孙业平 ; gromacs.org_gmx-users Subject:Re: [gmx-users] How to install gromacs on cpu cluster Hi Yeping, A full build may be

Re: [gmx-users] how to visualize gromacs trajectory

Hello, It sounds like you have to fixed broken molecules and have problem with boundary conditions. After doing the MD, you need to fix your trajectory first before doing visualization. Check this link for a workflow: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

[gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

Hello there are not parameters and RESP charges for standalone residue such as Arg in GROMACS. So you will have to construct a rtp file for this residue and derive the corresponding RESP charges yourself. You could also do a quick in literature to see if some have already done the job for

[gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells

Dear gmx-users, This is my first time running gromacs in a server (I mainly work on workstation) and I'm having some problems using efficiently more than a gpu per job. This is my script: #!/bin/bash -x #SBATCH --job-name=gro16AtTPC1 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=10 #SBATCH

Re: [gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells

Dear Mark, Thanks for the reply. I built the system using charmm-gui, and looking onto the *itp files of the protein, lipids, ions and water molecules (I forgot to mention that I’m simulating a protein channel embedded in a POPC membrane) I don’t see that line you mentioned

Re: [gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells

Hi, If you were using the [intermolecular_interactions] topology file section, there's a known bug that might have produced these symptoms. It's fixed in 2019.3, so if you think that might apply to you, please update the installation of GROMACS and let us know how you go! Mark On Tue, 2 Jul

Re: [gmx-users] simulation of water gradient across membrane protein

> On 2. Jul 2019, at 10:35, Phuong Tran wrote: > > Hi all, > > I was wondering if I can use the computational electrophysiology package in > Gromacs with the double membrane setup to simulate a system that has > different numbers of waters in and out. This would need to use the grand >

[gmx-users] Help with generating Arginine topology for Amber FF

Hi all, I'm trying to generate topology for arginine. I use the following command: gmx pdb2gmx -f Arginine.pdb -o Arg.gro -inter -water tip3p I get the following error: Fatal error: In the chosen force field there is no residue type for 'ARG' as a standalone (starting & ending) residue Please

[gmx-users] No compatible domain decomposition

Hello, I am trying to run a protein simulation consisting of ~100.000 atoms (box dimensions: 8.8x8.8x9.4nm) on multiple mpi threads. For the protein, I need to define a few distance restraints. Right now, these are defined with harmonic bonds in the  [ bond ] section of the protein: [ bonds ]

[gmx-users] simulation of water gradient across membrane protein

Hi all, I was wondering if I can use the computational electrophysiology package in Gromacs with the double membrane setup to simulate a system that has different numbers of waters in and out. This would need to use the grand canonical ensemble and the package is for ions only, and I don't know

Re: [gmx-users] a99SB-disp forcefield

Ask Paul, they have a Gromacs version of it and he'll most likely be happy to share it with you. J On Mon, Jul 1, 2019 at 8:19 PM Joe Greener wrote: > Dear Gromacs users, > > I am looking to use the a99SB-disp forcefield from Robustelli et al. > PNAS 2018

Re: [gmx-users] No compatible domain decomposition

Hi, If you express those as [intermolecular_interactions] then perhaps DD will cope better because it understands that they are intended to be handled separately. It doesn't matter that they are actually intramolecular! Mark On Tue., 2 Jul. 2019, 14:27 Daniel Bauer, wrote: > Hello, > > I am

Re: [gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

Do I still need to do this if I just want charged arginine (CARG)? Its my understanding that there are three types of arginine residues; ARG, CARG and NARG available. I thought the amino acids are available in gromacs? Sorry if it's a silly question to ask, but I have not used the Amber FF in

Re: [gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

On 7/2/19 12:01 PM, Pandya, Akash wrote: Do I still need to do this if I just want charged arginine (CARG)? Its my understanding that there are three types of arginine residues; ARG, CARG and NARG available. I thought the amino acids are available in gromacs? Sorry if it's a silly

Re: [gmx-users] simulation of water gradient across membrane protein

Thank you, Carsten. It’s good to confirm that. Phuong > On Jul 2, 2019, at 2:15 AM, Kutzner, Carsten wrote: > > > >> On 2. Jul 2019, at 10:35, Phuong Tran wrote: >> >> Hi all, >> >> I was wondering if I can use the computational electrophysiology package in >> Gromacs with the double

Re: [gmx-users] Error on scaling the charges

On 7/1/19 5:46 AM, Apramita Chand wrote: Dear Gromacs Users, I'm simulating an ionic liquid with AMBER 99sb-ildn ff in GROMACS 5.1.4 package. With charges +1 and -1 on the cation and anion respectively, the system is neutral and the minimization is okay. But on scaling the charges by 0.8, the

Re: [gmx-users] clustering of ions during NPT simulation

On 6/30/19 1:01 AM, Netaly Khazanov wrote: H Justin, I used amber99sb-ildn FF for the simulation. Which parameters do you suggest to use? I don't generally use AMBER so I can't comment on which parameters you should use, but this is a well-established (and solved) issue in the literature