Re: [gmx-users] Gromacs 2018.3 Exceeding Memory Issue

Hi, On Tue, Nov 27, 2018 at 4:31 AM Peiyin Lee wrote: > Hi, all GROMACS users, > >I am trying to run jobs with Gromacs 2018.3 version and constantly got a > memory exceeding error. The system I ran is an all-atom system with 21073 > atoms. The largest file that is estimated to be generated

Re: [gmx-users] preparing input file for GPU

Hi, You just need to not choose such groups. See http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#output-control Mark On Tue, Nov 27, 2018 at 7:10 AM Seketoulie Keretsu wrote: > I am running a protein ligand simulation for the first time after > installation of GPU.

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 95

Dear Alex Thank you for the "shameless self promotion". Have been looking for some classic gromacs products lately. Have seen some interesting methods in area of protein-ligand interactions. If you have some new and interesting gromacs papers related to Protein-ligand studies please suggest it

[gmx-users] preparing input file for GPU

I am running a protein ligand simulation for the first time after installation of GPU. When i execute mdrun i got this message, "Multiple energy groups is not implemented for GPUs, falling back to the CPU. ". I understand i have to remove the energy group in the .mdp file. But I am not sure how to

Re: [gmx-users] Charge system simulation problem

Hi Justin, Because I have self generated the itp file, and that's the only place where charge in terms of partial charge is added. Is the problem lying there? Also can't we denote the partial charges in decimal because in real some atoms will have net charges that can be decimal values due to

[gmx-users] Gromacs 2018.3 Exceeding Memory Issue

Hi, all GROMACS users, I am trying to run jobs with Gromacs 2018.3 version and constantly got a memory exceeding error. The system I ran is an all-atom system with 21073 atoms. The largest file that is estimated to be generated is around 5.8 GB. My jobs got constantly killed after running for

[gmx-users] shameless self-promotion

Hi all, This isn't a Gromacs question, but a bit of self-promotion with a not-so-hidden agenda. 1. Here's our paper that I think might be of interest to you beautiful biophysics folks: https://www.nature.com/articles/s41563-018-0220-4 2. All of this was done with Gromacs. I cannot imagine any

Re: [gmx-users] Interaction energy

Hi, On Mon, Nov 26, 2018 at 7:47 PM Nick Johans wrote: > On Mon, 26 Nov 2018, 21:28 Justin Lemkul > > > > > > On 11/26/18 10:51 AM, Nick Johans wrote: > > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul > > > > >> > > >> On 11/22/18 11:41 AM, Nick Johans wrote: > > >>> Hi > > >>> > > >>> I am

Re: [gmx-users] Distance calculation

Can i use -dist option? Would you please help me? On Mon, 26 Nov 2018, 00:48 rose rahmani Hi, > > My system contains 20 amino acids around nanotube. I want to know the > adsorption amount of AA during simulation time; the adsorption occurs > when the distance between one of non-hydrogen atoms of

[gmx-users] Parameterizing N-terminal capping

Hi I am trying to parameterize the N-terminal ‘carboxybenzyl’ capping for peptide within CHARMM force field. Charges and bonded terms are transferred by analogy from available amino acid and lipid parameters. Grompp throwing errors for missing dihedral and bond terms of the linkage between ester

Re: [gmx-users] Interaction energy

On Mon, 26 Nov 2018, 21:28 Justin Lemkul > > On 11/26/18 10:51 AM, Nick Johans wrote: > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul > > >> > >> On 11/22/18 11:41 AM, Nick Johans wrote: > >>> Hi > >>> > >>> I am beginner in MD. Maybe it is not a wise question but i want to > >>> calculate the

Re: [gmx-users] Interaction energy

On 11/26/18 1:35 PM, rose rahmani wrote: On Mon, 26 Nov 2018, 21:28 Justin Lemkul On 11/26/18 10:51 AM, Nick Johans wrote: On Mon, 26 Nov 2018, 18:22 Justin Lemkul On 11/22/18 11:41 AM, Nick Johans wrote: Hi I am beginner in MD. Maybe it is not a wise question but i want to calculate

Re: [gmx-users] Interaction energy

On Mon, 26 Nov 2018, 21:28 Justin Lemkul > > On 11/26/18 10:51 AM, Nick Johans wrote: > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul > > >> > >> On 11/22/18 11:41 AM, Nick Johans wrote: > >>> Hi > >>> > >>> I am beginner in MD. Maybe it is not a wise question but i want to > >>> calculate the

[gmx-users] -t state.cpt

Hi all, What would happen if someone would not use -t previous_state.cpt in the production run?? Isn't that the case that gromacs can read the velocity from the last frame .gro file of the previous simulation? Best -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Interaction energy

On 11/26/18 10:51 AM, Nick Johans wrote: On Mon, 26 Nov 2018, 18:22 Justin Lemkul On 11/22/18 11:41 AM, Nick Johans wrote: Hi I am beginner in MD. Maybe it is not a wise question but i want to calculate the interaction energy between protein and ligand and also PMF in different

Re: [gmx-users] Fwd: Mismatch between gromacs and python-networkx versions

On 11/26/18 12:54 PM, Francesco Pietra wrote: Hurrying - as with my post above - is seldom a good procedure. The next step, converting ligand_ini.pdb to ligand.gro did not work well, i.e., for GDP the .gro file reads S C A M O R G 40 0/scrPB1 0.100 0.000 0.100

[gmx-users] Fwd: Mismatch between gromacs and python-networkx versions

Hurrying - as with my post above - is seldom a good procedure. The next step, converting ligand_ini.pdb to ligand.gro did not work well, i.e., for GDP the .gro file reads S C A M O R G 40 0/scrPB1 0.100 0.000 0.100 0/scr O1B2 0.100 0.000 0.100 0/scr

Re: [gmx-users] pH Replica Exchange

As I guessed. Thanks. On Monday, November 26, 2018, Justin Lemkul wrote: > > > On 11/26/18 4:50 AM, Reza Esmaeeli wrote: > >> I’m considering Replica Exchange MD for different pH values with GROMACS. >> Any ideas where to start? >> >> (In the literature, this is usually done using Amber or

Re: [gmx-users] Mismatch between gromacs and python-networkx versions

This is to let you know, that the fixed .mol2 (got by first removing # comments, as you indicated), the script cgenff_charmm2gmx.py works well with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs with them, but the content of the files looks like to be what was expected. fp

Re: [gmx-users] rdf coordination number over time (ns)

Hi if you have rdf it is easy to calculate the coordination number by numerical integration https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions Arun On Mon, Nov 26, 2018 at 11:38 AM Maria Luisa wrote: > Dear users, > I need to calculate rdf coordination number

[gmx-users] rdf coordination number over time (ns)

Dear users, I need to calculate rdf coordination number over time. I have a pdb trajecory of 200 ns, from which I want to evaluate g(r) and CN of Na-Cl, Na-O, Cl-O. My gromacs works with VMD, but I cannot do coordination number in function of time! Can you help me? Maria Luisa Maria Luisa

[gmx-users] make_ndx and assigning velocities

Dear Gmx users, I have two questions. I am wondering how I can assign residues from different chains to one single index group? Say, residues 50 to 70 of first chain and residues 120 to 140 of the second chain. Secondly, how can I assign velocities to certain groups? For instance, to

Re: [gmx-users] Interaction energy

On Mon, 26 Nov 2018, 18:22 Justin Lemkul > > On 11/22/18 11:41 AM, Nick Johans wrote: > > Hi > > > > I am beginner in MD. Maybe it is not a wise question but i want to > > calculate the interaction energy between protein and ligand and also PMF > in > > different distances. But i don't know what

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 91

Dear Justin, Thanks for answer. On Mon, Nov 26, 2018 at 1:01 PM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit

Re: [gmx-users] ionize flag

On 11/26/18 8:34 AM, Elias Santos wrote: Hi everyone!! I'm working with a system in gas-phase, where in the first simulation I use the command mdrun -deffnm mdall -v. In the second one, it is bombarded with X-ray using the -[yes]ionize flag gromacs 4.5.6. However, comparing the two

Re: [gmx-users] pH Replica Exchange

On 11/26/18 4:50 AM, Reza Esmaeeli wrote: I’m considering Replica Exchange MD for different pH values with GROMACS. Any ideas where to start? (In the literature, this is usually done using Amber or CHARMM packages) Start by using AMBER or CHARMM :) AFAIK, there is no support for anything

Re: [gmx-users] Charge system simulation problem

On 11/26/18 12:01 AM, Karpurmanjari Kakati wrote: Dear All, My System contains, while doing NVT of the same, I got the following Note *NOTE 1 [file sa.top, line 80]: System has non-zero total charge: 12.936997 Total charge should normally be an integer. See

Re: [gmx-users] Mismatch between gromacs and python-networkx versions

On 11/25/18 9:10 AM, Francesco Pietra wrote: This is my first post to gromacs, to which I came in the hope that FEP simulations are more efficient than with other engines. I updated debian amd64 from stretch to buster in order to have the said preferred gromacs 2018 (2016 on stretch). Now,

Re: [gmx-users] sort_mol2_bonds.pl issues

On 11/26/18 2:46 AM, Francesco Pietra wrote: Hi sort_mol2_bonds.pl (taken from the 2018-updated protein-ligandb tutorial) does not work for me. The .mol2 file is simply stripped out of the whole list of bonds, while the atom list remain not ordered (for example oxygen before carbon, or C13

Re: [gmx-users] free binding energy calculation

On 11/23/18 4:07 PM, marzieh dehghan wrote: Thanks a lot for your kind answer, I used the same link to calculate free binding energy and confront the mentioned error. Please make sure to use a correct subject, and don't reply to the entire digest. If you're actively asking/answering

Re: [gmx-users] (no subject)

On 11/23/18 12:58 AM, maya nair wrote: I am trying to do the molecular dynamics of DNA-ligand complex. I made the ligand files using antechamber and converted the amber files to .gro and .top using acpype.pl. Then I made the complex.gro. when I am trying to run grommp ions.mdp and em.mdp,

Re: [gmx-users] Interaction energy

On 11/22/18 11:41 AM, Nick Johans wrote: Hi I am beginner in MD. Maybe it is not a wise question but i want to calculate the interaction energy between protein and ligand and also PMF in different distances. But i don't know what is the didference between PMF, i mean free energy in

Re: [gmx-users] Implementation of drude simulation

On 11/22/18 9:37 AM, Gonzalo Quezada wrote: Greetings gromacs users, I'm trying to run a simulation of polarizable water and ions with the drude-2013 forcefield. I use the simulation parameters from the supporting information from "Implementation of Extended Lagrangian Dynamics in GROMACS

Re: [gmx-users] Printing only center of mass of during simulation

On 11/22/18 6:39 AM, Sudarshan Behera wrote: Hello Gromacs Users, I wanted to know if there is any way to print only the *centre of mass* of a user defined group(instead of all the x,y,z coordinates) during simulation run (mdrun). There is no such feature. You can extract this information

[gmx-users] Gmx distance

Hi, I use gmx distance -dist 1.5 -f -s -n -o dist.xvg and select ZnS and Protein-H groups. Why i couldn't get any output file? Ot is processing during analuzing but it doesn't have any dist.xvg and output file. When i use option -lt the lifetime.xvg is empty. But i know there are distances closer

[gmx-users] ionize flag

Hi everyone!! I'm working with a system in gas-phase, where in the first simulation I use the command mdrun -deffnm mdall -v. In the second one, it is bombarded with X-ray using the -[yes]ionize flag gromacs 4.5.6. However, comparing the two simulations I have observed that the values for energies

[gmx-users] pH Replica Exchange

I’m considering Replica Exchange MD for different pH values with GROMACS. Any ideas where to start? (In the literature, this is usually done using Amber or CHARMM packages) Thanks, Reza -- Gromacs Users mailing list * Please search the archive at

[gmx-users] HOW TO EXTEND A .XTC FILE ??

Hello. I am running the MD simulations for 100ns using GROMACS software. Now, I have a .xtc file and  I would like to extend my simulation but not from final step. Could anyone suggest me how should I extend this .xtc file from specific frame for another 100ns and when it ended I just have one