[gmx-users] mdrun -c option "did not work"

Jérôme Baffreau jerome.baffreau at umontreal.ca
Fri Jun 26 08:44:10 CEST 2009

Thanks for your answer.

>> Actually no my run did not finish normally the first time (it has been 
>> stopped after 7 days because of the time limitation on the cluster it was 
>> running on). So I started it again (I ran the same command and added the 
>> option "-append yes") and this time the calculation finished normally, 
>> but when I look at the md.log file it looks like the second run did not 
>> add anything since it stops in the middle of a line (in the middle of a 
>> word actually!)...

> Sounds like a filesystem problem.

No, that's because the Linux cluster's system terminated my calculation when 
it reached max. allowed time.

>> Maybe I just did not use the correct command to start this calculation 
>> again, that would explain the end of the md.log and the "no-generation" 
>> of the final structure.
>> What option(s) should I use with trjconv? Actually I already tried to use 
>> this command, but it generated a 200 MB pdb file which was not my aim!

> Read trjconv -h and see how to choose the only final frame.

I have a stupid question: how do I know how many frames there are in my 

> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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


More information about the gromacs.org_gmx-users mailing list