Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Hi, Running gmx check -f your.file will tell you what is in your file. You can't get it to create data for the frames you have never saved anywhere. The nstxout option doesn't mean "save everything but later only show me frames at this interval" :-) Mark On Wed, 19 Oct 2016 07:58 Marko Sever

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Thanks. Still I was told that even if i set the "output frequency of frames" the .trr should contain more finer grained data? What file can I show you, that you can see more out from it? Regards, Marko -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] mpirun error

Thank you very much Andrew On Wed, Oct 19, 2016 at 10:31 AM, Andrew Guy wrote: > Hi Sun, > > In GROMACS 5.1, all the commands are under the gmx binary. You need to run > something like: > > >> source /your/installation/prefix/here/bin/GMXRC > >> mpirun -np $NPROCS gmx mdrun_mpi -s md.tpr -c npt.

Re: [gmx-users] mpirun error

Hi Sun, In GROMACS 5.1, all the commands are under the gmx binary. You need to run something like: >> source /your/installation/prefix/here/bin/GMXRC >> mpirun -np $NPROCS gmx mdrun_mpi -s md.tpr -c npt.gro -o md_0_1.trr Go and have a look at some tutorials which use GROMACS 5 or higher, and rea

[gmx-users] mpirun error

Dear Gromacs users and experts I am trying to run a test job of 1 ns remotely on supercomputer clusters. I have prepared .tpr file in my system (v 5.1.1) and submitted the script file on remote server. following is my script file: ###

Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2

On 10/18/16 12:20 PM, Chapman, Christopher W. wrote: Hi Mark, Yes, my implementation does work for standard parameter values. I agree with Mark. You likely have a bad parameter set, and mdrun is telling you it is crashing. Compute the forces in that trajectory and likely you will see wh

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Hi, Time gap of what? All this is set by your mdp options, so if you want help we're going to need to know what they are, and what makes you think what you've done "didn't work" :-) Mark On Tue, 18 Oct 2016 22:13 Smith, Micholas D. wrote: > Marko, > > 2fs timestep is your integration timestep,

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Marko, 2fs timestep is your integration timestep, not necessarily your frame saving rate. This is defined by your integration step multiplied by the nstxout term in your simulation mdp file. In order to save every integration step you would need to have dt = 0.001 (picseconds) and nstxout = 100

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Micholas, I think it should be 2fs the timestep if you are reffering to that? I have the .trr file its 95gb, I should be able to make a xtc with 1ps step right? Marko -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2

Hi Mark, Yes, my implementation does work for standard parameter values. Thanks, Chris -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Tuesday, October 18, 2016 11:55

Re: [gmx-users] gmx mdrun restart

Hi, There's no problem to fix. But you need to understand whether you're implementing what you want, because using -append and changing -deffnm is inconsistent. Mark On Tue, Oct 18, 2016 at 5:54 PM Sailesh Bataju wrote: > Hi, > > Thank you sir for your immediate response. So is there any way

Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2

Hi, This looks like one manifestation of "the model physics is broken, and so is the resulting simulation system." Does your implementation behave for standard parameter values? Mark On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. wrote: > Hello all, > > I am trying to model TIP4P/2005

Re: [gmx-users] gmx mdrun restart

Hi, Thank you sir for your immediate response. So is there any way that I can fix this problem expect not renaming file at different stages. If there is, help me with the command. Thank you for your consideration. -- Self-reliant is the great potential for success. -- Gromacs Users mailing lis

[gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2

Hello all, I am trying to model TIP4P/2005f water using Gromacs 5.1.2. Specifically, I'm trying to show how modifying the parameters of the TIP4P/2005f model changes the density of states. I wrote a small script to randomly vary the parameters and write out the .gro and .top files. When I tried

Re: [gmx-users] gmx mdrun restart

Hi, You're doing too much work. If you want appending (and generally you should, because all of our checks stop you making several of the many available silly errors :-) ), don't name each stage differently. Once you've forced it to write .edr files that are separate, then you have to use the conc

[gmx-users] gmx mdrun restart

Hi, I'm following tutorial of "Lysozyme in Water" and playing with mdrun, restarted several times as an experiment and got confusion whether the restart process may have effect on subsequent process. Here is what I did. Suppose nvt.tpr file is generated then 1st: gmx mdrun -deffnm nvt -v -maxh

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Hi Marko, Unless you saved your trajectory at a 1picosecond/frame saving rate, you won't be able to reduce the "gap" from 20ps to 1ps. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecu

Re: [gmx-users] Computational Electrophysiology: how about implicit solvent?

Hi Henry, > On 18 Oct 2016, at 14:45, Vries, de, H.W. > wrote: > > Dear all, > > > In the newest versions of GROMACS the computational electrophysiology > method (CompEL) is implemented through the swapping of solvent molecules > with ions, thus providing a constant transmembrane potential. >

[gmx-users] How to decrease the time gap between frames of an already made simulation

Hello, could you please advise regarding the correct command for decreaseing the time gap between frames of an already made simulation, from 20ps to 1ps. I tried these commands but they didn't work: gmx trjconv -s md.tpr -f md.trr -o md1pico.xtc -tu ps -skip 500 gmx trjconv -f md.trr -o md1p

[gmx-users] Computational Electrophysiology: how about implicit solvent?

Dear all, In the newest versions of GROMACS the computational electrophysiology method (CompEL) is implemented through the swapping of solvent molecules with ions, thus providing a constant transmembrane potential. However, I am currently employing an implicit solvent model. My question therefo

Re: [gmx-users] Thermodynamic integration and re-weighting method

Hi Alex, I thought by getting the flat-bottom restraint potential on my target molecule I should be able to get the free energy of unbiased case. Basically; P(q)=P’(q)exp(V(q)/kBT) Here P is unbiased probability, P’ is biased probability and V is added potential. However I am not totally sure.

Re: [gmx-users] pressure coupling

Hi, IIRC you can set pcoupl to semiisotropic, set the x/y compressibility (or tau-p?) to 0, and set z to what you want it to be. Peter On 17-10-16 21:45, pari lotfi wrote: > Dear all, > > How can I simulate a box of water in NATPz condition? > In this simulation, particle number N, surface ar