[gmx-users] Whether my simulation is conserved?

Dear gromacs users, I have done simulations for 100ns. To know whether my simulation is conserved, I have preferred to do simulated annealing. I have set the highest temperature as 350K at 25ns and allowed it go down to room temperature 300K at 50ns. And eventually I executed the mdrun for 50ns

[gmx-users] Regarding calculation of Lennard-Jones potential

Hello, I have a simulation mixture of aminoacid (eg., glycine) with water and cosolvent. I want to calculate Lennard-Jones Parameters of the all atom types. How can i calculate it...?? Can it be done with commands, or any other method..?? Any suggestions are appreciated... Thank you.. -- With

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

Thank you for your reply. When I try to run my job in a single processor through qsub command, (by feeding the gromacs mdrun command in script file), it says SEGMENTATION FAULT, CORE DUMPED... But, when I run my job in login node (which we are not supposed to do), it works very well... Can

Re: [gmx-users] Changes in the simulation box after the production run

These two images will help you see what is going on: https://twitter.com/dr_dbw/status/909559339366572032 - shows a molecule that appears to be outside the box. https://twitter.com/dr_dbw/status/909559783291723776 - however, that molecule actually enters through the opposite face of the box.

Re: [gmx-users] Changes in the simulation box after the production run

Thank you for you quick reply, Justin and Dallas! Very good point! Best regards, Mahsa On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul wrote: > > > On 9/17/17 6:57 PM, Mahsa E wrote: > >> Could you please see the link below for the input and output simulation >> box: >> >>

[gmx-users] Cloud based molecular simulations

Hello, We have been hard at work and are now ready to let the public test our intial product offering. Please check our web based molecular simulations platform at https://ioniclabs.io. At Ionic Labs you can run your simulations in two ways: 1. By creating a workstation which has a

Re: [gmx-users] Changes in the simulation box after the production run

On 9/17/17 6:57 PM, Mahsa E wrote: Could you please see the link below for the input and output simulation box: https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0 Actually, I thought since some of the chains went out of the simulation box, then density have been

Re: [gmx-users] Changes in the simulation box after the production run

Could you please see the link below for the input and output simulation box: https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0 Actually, I thought since some of the chains went out of the simulation box, then density have been changed. In my previous experience with

Re: [gmx-users] Diffusion coefficient

On 9/17/17 6:05 PM, Dallas Warren wrote: http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html Don't know exactly how to do it myself, but there will be an option there where you can specify the z coordinate as a way to break it up into groups. And herein lies the

Re: [gmx-users] Changes in the simulation box after the production run

Because that is how the system changed within the simulation time? What exactly is the problem as you see it, and why do you think it is a problem? And remember, you have a periodic boundary condition that means the one edge of the box wraps around to the opposite one. So "out of the box" is a

Re: [gmx-users] Diffusion coefficient

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html Don't know exactly how to do it myself, but there will be an option there where you can specify the z coordinate as a way to break it up into groups. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

Hi, You're running a thread-MPI version of GROMACS, which is probably not what you want to do if you're running mpirun. It should work even so, but whatever quirks exist with SGE are unfortunately between you, its docs and your cluster's docs and admins :-( Mark On Sun, Sep 17, 2017 at 7:23 AM

[gmx-users] Changes in the simulation box after the production run

Dear gmx-users, I did a 200 ns production md run in NVT ensemble for a simulation box of polymer chains. Before this step, I did the energy minimisation, NVT and NPT equilibration on the system. The problem is after the production run, I don't get the initial equilibrated packed box of polymer

Re: [gmx-users] how to generate a trr file

Hi, You can use "trjconv" command and specify "-e 5". Hope it helps!! Regards, Subhomoi B. On 17 Sep 2017 8:34 pm, "marzieh dehghan" wrote: > Dear all > Hi > > I performed molecular dynamics simulation during 100 ns, but now I want to > create a trr or xtc

[gmx-users] unsatisfactory result for kinetic energy using trj ekt and ekr

Hi Everyone, I want to calculate the kinetic energy of a particular group. I use gmx trj ekt and ekr to calculate translational and rotational kinetic energy. But the result I obtained doesn't look correct. As I choose larger groups (even the smaller group is a subset of larger group) total

[gmx-users] how to generate a trr file

Dear all Hi I performed molecular dynamics simulation during 100 ns, but now I want to create a trr or xtc file including 50 ns. how I can generate trajectory file containing 50 ns from 100 ns of MD run? thanks a lot best wishes -- *Marzieh DehghanPhD of BiochemistryInstitute of

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU /view?usp=sharing=59be86ad On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul wrote: > > > On 9/17/17 1:22 AM, Vidya R wrote: > >> My log file is provided in the link below >> >> Can you please look into it and let me

[gmx-users] gromacs-error.docx

I've shared an item with you: gromacs-error.docx https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU/view?usp=sharing=59be86ad It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

On 9/17/17 1:22 AM, Vidya R wrote: My log file is provided in the link below Can you please look into it and let me know why the error arises? I am feeding my commands in SGE cluster. When I run it in my login node, gmx mdrun -v -deffnm eql runs well But, through qsub command, (with 8