OZGE ENGIN wrote:
This time, I used the following command line:
mpirun -np 8 mdrun_mpi -s simul0_md.tpr -replex 2500 -reseed -1 -multi 8
rename
rename your tpr files to
simul_md0.tpr
simul_md1.tpr
...
simul_md7.tpr
but I got the following error:
Program mdrun_mpi, VERSION 3.3.99_development_20070413
Source code file: gmxfio.c, line: 706
Can not open file:
simul00.tpr
-------------------------------------------------------
"Shit Happens" (Pulp Fiction)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
Although I do not have such a file: simul00.tpr
-----Original Message-----
From: "Berk Hess" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:58:48 +0100
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
You need to supply the -np option.
In Gromacs 3.3 you don't need to set the -multi option,
and -multi does not take an argument.
If you use the CVS head branch, you need to set -np and -multi
both with an argument.
Berk.
From: "OZGE ENGIN" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@gromacs.org
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange
MD
Date: Fri, 23 Nov 2007 11:44:47 +0200
Hi Berk,
I indicated the number of replicas with -multi option. In additon, I have
compiled Gromacs with MPI support.
I used the following command line:
mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500
-----Original Message-----
From: "Berk Hess" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:36:57 +0100
Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD
From: "OZGE ENGIN" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@gromacs.org
Subject: [gmx-users] problem with mdrun performing replica exchange MD
Date: Fri, 23 Nov 2007 11:30:53 +0200
Hi All,
I am performing replica exchange molecular dynamics simulation(REMD). I
have 16 replicas each of which has a peptide with different conformation.
After obtaining .tpr files (at desired temperatures) for each replicas, I
loaded them via mdrun, but I got the following error:
Fatal error:
Nothing to exchange with only one replica
-------------------------------------------
Why?
I guess there are two possibilities.
Or you did not use the -np option of mdrun to set the number of replicas,
or you have not compiled Gromacs with MPI support.
Berk.
_________________________________________________________________
Talk with your online friends with Messenger
http://www.join.msn.com/messenger/overview
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
Play online games with your friends with Messenger
http://www.join.msn.com/messenger/overview
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
