Re: [gmx-users] issue regarding gromacs software

On 2/15/19 12:17 PM, suchita sakore wrote: Respected sir/madam, I am doing a project under my post graduation. I am doing a simulation of a lipid ion channel by using gromacs software. I am facing problem while generating the gro file. I have built peptide by using discovery studio software.

Re: [gmx-users] centroid distance for tyrosine

On 2/15/19 2:37 PM, Archana Sonawani-Jagtap wrote: Hi, I want to calculate centroid distance between 2 tyrosine rings throughout the simulation. Which option of gmx distance can help to plot the centroid distance? Create two index groups with the ring atoms, then use gmx distance: gmx

[gmx-users] centroid distance for tyrosine

Hi, I want to calculate centroid distance between 2 tyrosine rings throughout the simulation. Which option of gmx distance can help to plot the centroid distance? Thanks, Archana -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Make check not passing tests on 2018.5

You compiled gcc from sources? From which sources (e.g. tgz or deb-src, any patches?) How did you compile gcc (your configure arguments)? Could you try with GMX_FFT_LIBRARY=fftpack or with the fftw provided by the system by running cmake without GMX_BUILD_OWN_FFTW? Want to make sure it isn't

Re: [gmx-users] issue regarding gromacs software

I do not see the attachment... Which forcefield are planning to use? In any case you should check the input pdb you are using: are the amino acid residues named in the proper way? It is a standard pdb? Do you have some non-natural amino acid or modified residue in your peptide? Moreover you

Re: [gmx-users] Make check not passing tests on 2018.5

That's quite interesting, I wonder what it is about my system that is causing the issue. If it means anything, this is on a fresh install of Ubuntu 18.04. I've had a chance to experiment with compilers on my system. GCC 8.2.0 passes with avx-512. Using a freshly compiled version of GCC 7.3.0 and

[gmx-users] issue regarding gromacs software

Respected sir/madam, I am doing a project under my post graduation. I am doing a simulation of a lipid ion channel by using gromacs software. I am facing problem while generating the gro file. I have built peptide by using discovery studio software. while running the following command : gmx_mpi

Re: [gmx-users] Interaction energies between atoms

Hello. Yo can do int with g_energy. Before of using this command, you need to add that atom and its interactor (separately) to an index file using make_ndx. Best regards. On Fri, 15 Feb 2019 10:36:20 +0100, Mark Abraham wrote: Hi, How would you define that interaction energy? What would you

Re: [gmx-users] AWH with two bias potentials

Your force constant is high which means you get many grid points, especially in 2D. If possible, you should decrease it. Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cédric Leyrat Sent: Friday, February 15, 2019 4:36 PM To:

Re: [gmx-users] AWH with two bias potentials

Thanks a lot for all the helpful information, I will decrease the initial error and increase the diffusion. Actually before seeing your email I had modified my .mdp file like this, which made mdrun behave better (although the .edr file is still very large - about 7GB after 5 hours): awh  

Re: [gmx-users] AWH with two bias potentials

Your initial error parameters is orders of magnitude too large. You don't expect an error of 1 kJ/mol, or do you? 10 is more reasonable. The initial update size depends on this error squared. Likely your diffusion parameters are one or two order of magnitude too small, so you should increase

[gmx-users] GROMACS 2019.1 patch release available

Hi GROMACS users, The official release of GROMACS 2019.1 is available! This first patch release fixes several issues found since the initial release of GROMACS 2019. We encourage all users of the 2019 series to update to 2019.1. Please see the link to the release notes below for more details.

Re: [gmx-users] Select one molecule closest to another molecule for all snapshots

On 2/15/19 4:10 AM, Apramita Chand wrote: Dear Gromacs Users, I have two kinds of molecules in my system. I want to know the coordinates of the molecule A that is found closest to molecule B at every snapshot of the MD trajectory. I am using gromacs 5.1. I dont have a cutoff, I just want to

Re: [gmx-users] Gromacs Group Project Force-Field Query

On 2/15/19 8:39 AM, Matthew Atkinson wrote: Dear all, We are currently working on a project at the University of Manchester, which involves using GROMACS to understand the molecular dynamics of the biological machines for the walkers dynein and kinesin. However, when using the command

Re: [gmx-users] How to calculate distance using gromacs?

On 2/15/19 8:16 AM, Edjan Silva wrote: Dear, I performed a 100 ns simulation with B-DNA. I want to know which gromacs option I can calculate the distance between two DNA residues (guanine 5 and ADENIN 6, for example) during the 100 ns of simulation. Create an index group for each

[gmx-users] Gromacs Group Project Force-Field Query

Dear all, We are currently working on a project at the University of Manchester, which involves using GROMACS to understand the molecular dynamics of the biological machines for the walkers dynein and kinesin. However, when using the command gmx_d pdb2gmx -f 5nvu_clean.pdb -o

Re: [gmx-users] How to calculate distance using gromacs?

Hello, You can do it with gmx mindist, but first you need to make two index group of the two residues. All the best, Qinghua On 2/15/19 2:16 PM, Edjan Silva wrote: Dear, I performed a 100 ns simulation with B-DNA. I want to know which gromacs option I can calculate the distance between

[gmx-users] How to calculate distance using gromacs?

Dear, I performed a 100 ns simulation with B-DNA. I want to know which gromacs option I can calculate the distance between two DNA residues (guanine 5 and ADENIN 6, for example) during the 100 ns of simulation. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Make check not passing tests on 2018.5

Forgot to get back, but same here, I checked on a Core i9 with gcc 7.3 (compiled from source though) and could not reproduce it. -- Szilárd On Thu, Feb 14, 2019 at 6:36 PM Schulz, Roland wrote: > I can't reproduce this. For me the regressiontests pass with gcc 7.3, > AVX_512, double. > >

Re: [gmx-users] help for debye waller factor calcuations

"gmx msd" is the command you need to use. DWF is defined as MSD at caging time. first define a caging time of your material, and then take MSD corresponds to it. see this literature https://pubs.acs.org/doi/10.1021/acs.macromol.6b00121 Chi Zhang PhD candidate, ETH Zurich

Re: [gmx-users] Interaction energies between atoms

As Mark mention, I also don't know what would I learn from its value but if you want, you can define two groups, each group contains the index of the atom that you want to calculate. In .mdp file, add this line: energygrps = NAME_OF_GROUP_1 NAME_OF_GROUP_2 On Fri, Feb 15, 2019 at 10:36 AM Mark

Re: [gmx-users] Unability to generate toplogy files for T3 & T4 residues from 4lnx.pdb

Hi, On Fri, 15 Feb 2019 at 01:39 Denish Poudyal wrote: > The universal force field is also not working. There is no universal force field supported in GROMACS, so I'm not sure what you mean. > how can I generate > parameters for such hetero-clusters via gromacs? > I don't know what T3 and

Re: [gmx-users] Interaction energies between atoms

Hi, How would you define that interaction energy? What would you learn from its value? Mark On Fri, 15 Feb 2019 at 02:26 Sam David wrote: > Hello GMX users, > I'm simulation a mixture of polymers, water, and hydrocarbons. I want to > calculate the interaction energies of an atom in one of the

[gmx-users] Select one molecule closest to another molecule for all snapshots

Dear Gromacs Users, I have two kinds of molecules in my system. I want to know the coordinates of the molecule A that is found closest to molecule B at every snapshot of the MD trajectory. I am using gromacs 5.1. I dont have a cutoff, I just want to generate coordinates of the single one molecule