[gmx-users] Restart

[Alok]

Hello Mark,

tpbconv is also used to extend the simulation run time.

try 

a) tpbconv -h

or

b) tpbconv -s original.tpr -f original.trr -e original.edr. -o new.tpr -extend 750
 
you will get new.tpr file. Use this new.tpr file for the mdrun program for the continuation of your simulation till 1.5ns


Alok
  ----- Original Message ----- 
  From: Mark Zottola 
  To: Discussion list for GROMACS users 
  Sent: Sunday, August 19, 2007 11:17 PM
  Subject: Re: [gmx-users] Restart


  Dil,

  Thanks for the post.  However, my original job was set for 750 ps and ran successfully.  Now, I would like to run an additional 750 ps.  The tbpconv seems more for restarting after a crash or modifying the original system.  I only want to achieve a 1.5 ns simulation.  So my questions remain.

  Thanks,


  Mark

   
  On 8/19/07, Dilraj Lama <dennis at iitk.ac.in> wrote: 

    > I know this will get an rtfm response, however, I am writing this after
    > looking at the online help pages and perusing the email archive. 
    >
    > Simply put, I have a 750 ps simulation that I want to run for another 750
    > ps.  Is there a clear explanation somewhere for how one should do this?

    use tpbconv with -extend option

    > Specifically, if I shut off the gen_vel option in my mdp file and use the 
    > the "-t" option to specify my first trajectory file are these the only
    > changes necessary?  If I keep all other options identical will I get the
    > 750
    > ps continuation I desire?

    There is no need to change the mdp file.Have a look at the tpbconv options.
    >
    > Thanks for the help.
    >
    >
    > Mark
    > _______________________________________________
    > gmx-users mailing list     gmx-users at gromacs.org
    > http://www.gromacs.org/mailman/listinfo/gmx-users
    > Please search the archive at http://www.gromacs.org/search before posting!
    > Please don't post (un)subscribe requests to the list. Use the
    > www interface or send it to gmx-users-request at gromacs.org.
    > Can't post? Read http://www.gromacs.org/mailing_lists/users.php


    --
    Dilraj Lama,
    Graduate student, 
    Bioinformatics and Biomolecular Simualtion lab,
    Dept. of BSBE;IITK-kanpur,
    Uttar pradesh,India-208016.
    email:dennis at iitk.ac.in, dilraj2002 at yahoo.com
    mob:09415473973

    _______________________________________________
    gmx-users mailing list    gmx-users at gromacs.org
    http://www.gromacs.org/mailman/listinfo/gmx-users
    Please search the archive at http://www.gromacs.org/search before posting!
    Please don't post (un)subscribe requests to the list. Use the 
    www interface or send it to gmx-users-request at gromacs.org.
    Can't post? Read http://www.gromacs.org/mailing_lists/users.php 





------------------------------------------------------------------------------


  _______________________________________________
  gmx-users mailing list    gmx-users at gromacs.org
  http://www.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at http://www.gromacs.org/search before posting!
  Please don't post (un)subscribe requests to the list. Use the 
  www interface or send it to gmx-users-request at gromacs.org.
  Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070819/011efd79/attachment.html>