Re: [gmx-users] Script for looping n simulations

Eappen Sent: Saturday, February 22, 2020 4:28 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Script for looping n simulations Thank you Miro, but I don't think I found what I wanted in your script. Let me be more clear: I ran n simulations in a loop, I have

Re: [gmx-users] Script for looping n simulations

thanks, Neena From: Neena Susan Eappen Sent: Saturday, February 22, 2020 4:28 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Script for looping n simulations Thank you Miro, but I don't think I found what I wanted in your script. Let

Re: [gmx-users] Script for looping n simulations

://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts -Justin Thank you for your time and knowledge, Neena From: Neena Susan Eappen Sent: Saturday, February 15, 2020 4:44 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Script

Re: [gmx-users] Script for looping n simulations

From: Neena Susan Eappen Sent: Saturday, February 22, 2020 2:41 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Script for looping n simulations Thank you Justin, just sharing the sample script here: #!/bin/bash for i in {1..n} do

Re: [gmx-users] Script for looping n simulations

I have something like this on my github. https://github.com/Miro-Astore/gromacs_scripts/tree/master/pbs_files/gadi File is memb0.pbs let me know if you have any questions. On Sat., 15 Feb. 2020, 8:45 am Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > >

Re: [gmx-users] Script for looping n simulations

, February 15, 2020 4:44 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Script for looping n simulations Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from

Re: [gmx-users] Script for looping n simulations

On 2/15/20 11:44 AM, Neena Susan Eappen wrote: Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. It's the same logic as in

[gmx-users] Script for looping n simulations

Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. Many thanks, Neena -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Script to merge protein and ligand topology for BAR calculation?

Hi Christian, Thank you for the link! We have written a script locally, was wondering if one existed elsewhere though! Thanks again for your help, Billy On Wed, 13 Nov 2019 at 05:52, Christian Blau wrote: > Hi Billy, > > > I cannot offer a script for the merging of the topologies, but

Re: [gmx-users] Script to merge protein and ligand topology for BAR calculation?

Hi Billy, I cannot offer a script for the merging of the topologies, but depending on the transformation you want to carry out, I can suggest using pmx http://pmx.mpibpc.mpg.de/webserver.html for preparing dual topologies for alchemical free energy calculations that are

[gmx-users] Script to merge protein and ligand topology for BAR calculation?

Hi Experts, I have a protein .itp file I -also- have the dual ligand .itp file to perform a relative alchemical transformation Both are compatible with GROMACS, and use AMBER/GAFF parameters. I need a script that can easily merge the two together. Have been doing on Excel. I was wondering if

Re: [gmx-users] script

You could use a sed command in your script to replace that line, something like sed "s/original expression/new expression/" filename -i But it depends a lot on how your mdp file is formatted in terms of spaces and tabs. Hope it helps, On Thu, 7 Mar 2019, 12:14 Amin Rouy, wrote: > Hi > > I

Re: [gmx-users] script

a dirty way: grep -v ref_t npt.mdp >new.mdp && echo -e "ref_t=300" >>new.mdp sorry again! On Thu, Mar 7, 2019 at 6:16 PM Amin Rouy wrote: > It is fine. > My question was not about '.mdp' itself. I meant how to define the > 'Temperature' inside the bash scrip, to avoid changing it by opening

Re: [gmx-users] script

It is fine. My question was not about '.mdp' itself. I meant how to define the 'Temperature' inside the bash scrip, to avoid changing it by opening the .mdp file. On Thu, Mar 7, 2019 at 4:57 PM Quyen Vu wrote: > Dear all, > It's my fault that I have un-nice behavior, I'm so sorry for that. >

Re: [gmx-users] script

Dear all, It's my fault that I have un-nice behavior, I'm so sorry for that. If I understand correctly, you are working with Gromacs so you should understand what is the .mdp file used for and there, the document of temperature section talk about that. On Thu, Mar 7, 2019 at 4:06 PM Amin Rouy

Re: [gmx-users] script

Thank you Justin. Yes, Quyen I've read the manual. I got helps from Justin's scrips in his tutorial page (great source) and googled before I came to write here. On Thu, Mar 7, 2019 at 4:01 PM Justin Lemkul wrote: > > > On 3/7/19 9:56 AM, Quyen Vu wrote: > > my question for you: have you ever

Re: [gmx-users] script

This is a welcoming and friendly community, with somewhat busy but still nice people. The manual is available at: http://manual.gromacs.org/documentation/ One can search for temperature information here: http://manual.gromacs.org/documentation/current/reference-manual/index.html to find :

Re: [gmx-users] script

On 3/7/19 9:56 AM, Quyen Vu wrote: my question for you: have you ever read gromacs manual/documentation? Where in the GROMACS manual do we discuss how to use Linux commands to alter scripts in this way? Please do not simply dismiss others' questions; it is not productive and not helpful.

Re: [gmx-users] script

my question for you: have you ever read gromacs manual/documentation? On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy wrote: > Hi > > I would like to change the temperature of the simulation (NPT.mdp) inside > my bash script, any one has idea? > thanks > -- > Gromacs Users mailing list > > * Please

[gmx-users] script

Hi I would like to change the temperature of the simulation (NPT.mdp) inside my bash script, any one has idea? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation

...@gromacs.org Subject: Re: [gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation Hi, You can do this using built-in gromacs tools. You want to make a suitable index group using gmx make_ndx, after which you can use gmx distance to measure

Re: [gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation

Hi, You can do this using built-in gromacs tools. You want to make a suitable index group using gmx make_ndx, after which you can use gmx distance to measure the distance between your groups. Dries On 13 Apr 2016 3:50 p.m., "Faulkner, Matthew" wrote: > Hi all, > >

[gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation

Hi all, Does anybody have a script, or reference where this has been done, for measuring distances between two residues in each time step of a simulation and exporting this data into a handy format like a text or csv file? I want to measure the distances over time between the nearest atoms of

Re: [gmx-users] Script to submit the md simulations on cluster.

Hi, No, we can't. Every cluster is set up differently. You have to consult your local documentation and sysadmins. That said, shell scripts tend to prefer NAME=value ie without spaces Mark On Mon, Aug 24, 2015 at 7:28 AM Seera Suryanarayana paluso...@gmail.com wrote: Dear gromacs users, I

[gmx-users] Script to submit the md simulations on cluster.

Dear gromacs users, I would like to submit the mdrun on cluster. I have written a shell script for submission as following. EXECUTABLE=./mdrun_mpi465 ARGUMENTS = -v -deffnm md_0_1.tpr INPUT_FILES = file:///home/suryanarayana1599/md.mdp, file:///home/suryanarayana1599/npt.cpt,