Re: [gmx-users] Ion pair

On 07/09/17 03:38, Tuanan Lourenço wrote: Hi everybody, I am working with electrolytes simulations using Gromacs, so I am trying to get the residence time (ion pair lifetime, ion cage lifetime) of the ions. I tried to use gmx hbond with the option -contat, but if try get the acf of the

[gmx-users] Running multiple Gromacs simulations on the same node

Hi all, It may seem a bit weird, but I'm trying to run multiple Gromacs simulations simultaneously on the same node, and I specified each Gromacs simulation to use only 1 MPI process and 1 OMP thread. I'm doing this because I am trying to check how accurate my model can predict an application

Re: [gmx-users] Ion pair

Hi Tuanan, although it's not a distributable/documented code, I have an old Fortran program (dating back to my PhD days) that does just that. Please feel free to contact me off the list if you think it might be of any use to you. best André On Wed, Sep 6, 2017 at 10:38 PM, Tuanan Lourenço

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 20

On 9/7/17 4:09 PM, vijayakumar gosu wrote: I have used below mdrun command taskset -c 0-79 gmx mdrun -deffnm md_0_1 -v i am not sure whether i have to apply mpi threads. To communicate between nodes, yes. Be sure you read

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 20

I have used below mdrun command taskset -c 0-79 gmx mdrun -deffnm md_0_1 -v i am not sure whether i have to apply mpi threads. Virus-free. www.avg.com

Re: [gmx-users] gromacs installation

On Thu, Sep 7, 2017 at 3:25 PM, vijayakumar gosu wrote: > Hi, > > I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus. > I am allotted to use only 2 nodes with 80 cpus. after installation when i > did sample md run only 20 cpus are being

[gmx-users] gromacs installation

Hi, I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus. I am allotted to use only 2 nodes with 80 cpus. after installation when i did sample md run only 20 cpus are being utilized. How can I fully utilize the all 80 CPUs for mdrun. I have used below cmake command for the

Re: [gmx-users] purpose of step pdb files during MD

On 9/7/17 10:29 AM, Vedat Durmaz wrote: i really appreciate this pretty informative answer. and do you also know, what the infix "n254" or "n2" stands for? Node ID. what i found strange is that the error occurs after nearly 10M MD steps. in other copies of the same system, the error

Re: [gmx-users] Merging different topology files

On 9/7/17 10:19 AM, Momin Ahmad wrote: Hello all, is there a simple way to merge two or more topology files into one? I am trying to use grompp to set up a simulation but my solvation contains different molecules which have different .top files. I also tried creating a main topology file

[gmx-users] Diffusion coefficient

Hey Users, I want to calculate the diffusion coefficient using gmx msd. I want to divide the box into slices of 5 A parallel to z axis and calculate the diffusion coefficient for each slice. My question is how to make these slices, I've tried gmx trajconv but didn't work with me. I believe it's

Re: [gmx-users] Incorrect link for release notes of gromacs 2016.3

Fixed it, thanks Åke! -- Szilárd On Thu, Sep 7, 2017 at 6:36 PM, Åke Sandgren wrote: > Hi! > > The link for the release notes of gromacs 2016.3 on www.gromacs.org is > pointing to 2016.1 > > -- > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden > Internet:

[gmx-users] Incorrect link for release notes of gromacs 2016.3

Hi! The link for the release notes of gromacs 2016.3 on www.gromacs.org is pointing to 2016.1 -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se -- Gromacs

Re: [gmx-users] purpose of step pdb files during MD

i really appreciate this pretty informative answer. and do you also know, what the infix "n254" or "n2" stands for? what i found strange is that the error occurs after nearly 10M MD steps. in other copies of the same system, the error doesn't occur at all even after the entire predefines time

[gmx-users] Fwd: Merging different topology files

weird, my email got cut off Weitergeleitete Nachricht Betreff:Merging different topology files Datum: Thu, 7 Sep 2017 16:19:29 +0200 Von:Momin Ahmad An: gmx-us...@gromacs.org Hello all, is there a simple way to merge two or more

[gmx-users] Merging different topology files

Hello all, is there a simple way to merge two or more topology files into one? I am trying to use grompp to set up a simulation but my solvation contains different molecules which have different .top files. I also tried creating a main topology file which includes the other two topologies

Re: [gmx-users] gromacs ligand topology file for "GNP"

On 9/7/17 9:23 AM, Deep kumar wrote: Hello, On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul wrote: On 9/6/17 3:46 PM, Deep kumar wrote: Dear All, I have produced the "ITP" files of the ligands using ATB server. I am mentioning the steps here, please let me know if you

Re: [gmx-users] gromacs ligand topology file for "GNP"

Hello, On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul wrote: > > > On 9/6/17 3:46 PM, Deep kumar wrote: > >> Dear All, >> >> I have produced the "ITP" files of the ligands using ATB server. I am >> mentioning the steps here, please let me know if you think anything is >> wrong.

Re: [gmx-users] DPOSRES not working

I cant say I fancy one who wants make money on knowing what on other peoples mind, but that does not mean you are the same! :) I think this worked out, but what the "bug" may be, that after doing 5 simulations twice, each time the confout.gro is something different from the confout.gro that

Re: [gmx-users] DPOSRES not working

On 9/7/17 8:52 AM, Sergio Manzetti wrote: Hey Justin , you sound like Mark Zuckerberg :) I don't know whether that's good or bad... Here is the command I used: gmx trjconv -f traj -o confout5000.gro -b 1 -e 1 -dump 1 is easier than using -b and -e, FYI. and it gives the

Re: [gmx-users] DPOSRES not working

Hey Justin , you sound like Mark Zuckerberg :) Here is the command I used: gmx trjconv -f traj -o confout5000.gro -b 1 -e 1 and it gives the write gro with DNA in the box as it should be. This confout.gro is not the same as came out from the GMX run, at the same moment as the TRJ

Re: [gmx-users] DPOSRES not working

On 9/7/17 8:45 AM, Sergio Manzetti wrote: It seems that GMX simply didn't write out the correct frame. The confout.gro file written out is written at the same time as the trajectories, and for some reason, this confout.gro file has nothing to do with the last output frame from the sims,

Re: [gmx-users] DPOSRES not working

It seems that GMX simply didn't write out the correct frame. The confout.gro file written out is written at the same time as the trajectories, and for some reason, this confout.gro file has nothing to do with the last output frame from the sims, when produced by gmx trjconv.. Sergio

Re: [gmx-users] DPOSRES not working

On 9/7/17 5:28 AM, Sergio Manzetti wrote: Hi Johannes, yes, they are there in both cases: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif Do you have a position restraint energy term written in your .log file, and if so, what is its magnitude?  Does

Re: [gmx-users] purpose of step pdb files during MD

On 9/6/17 5:55 AM, Vedat Durmaz wrote: hi guys, from time to time i'm faced with GMX output files during MD called, e.g. in the current case: step8164372b_n254.pdb step8164372b_n2.pdb step8164372c_n254.pdb step8164372c_n2.pdb what i know is that they are related to kind of exploding

Re: [gmx-users] selecting atoms in index file

On Thu, Sep 7, 2017 at 12:35 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] DPOSRES not working

Hi Johannes, yes, they are there in both cases: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun

Re: [gmx-users] DPOSRES not working

Okay, but what did you define in your topologies for your DNA chains: #include "topol_DNA_chain_E.itp" #include "topol_DNA_chain_F.itp" Make sure that at the end of these files you have lines stating e.g: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif

Re: [gmx-users] DPOSRES not working

Hi Johannes, it appears so: ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_DNA_chain_E.itp" #include "topol_DNA_chain_F.itp" #include "PRB_GMX.itp" ; Include water topology #include "amber99sb-ildn.ff/spc.itp"

Re: [gmx-users] DPOSRES not working

Dear Sergio, how did you define the position restrain in your topology? Check your topology and position restrain file. All the best Johannes On 07.09.2017 11:07, Sergio Manzetti wrote: Hello, I am running 5 simulations with the given mdp: title = DNA in water stabilization cpp =

Re: [gmx-users] selecting atoms in index file

Dear Golnaz, do you know the number (index) of the respective atoms? E.g. open the .gro file in vmd and look for the atoms? If there are not too many atoms, you can manually edit your index file. E.g. create a default index file (gmx make_ndx) and add the subset of indexes with a new

[gmx-users] DPOSRES not working

Hello, I am running 5 simulations with the given mdp: title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = -DPOSRES integrator = md dt = 0.002 nsteps = 1000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 300 nstxout-compressed = 300

[gmx-users] selecting atoms in index file

Dear All, I want to create an index file and select some especial atoms in a surface. My problem is that I have only one residue for the whole surface. How can I select the atoms on the surface as a different groups in my index file? Thank you in advance, Golnaz -- Gromacs Users mailing list *

Re: [gmx-users] purpose of step pdb files during MD

Energy minimization output explains them. I do not think they are important if you get good energy minimization after all. On Thursday, September 7, 2017, 3:41:59 AM GMT+3, Vedat Durmaz wrote: hi guys, from time to time i'm faced with GMX output files during MD