AMBER Archive (2008)

Subject: Re: AMBER: replica exchange : problem with sander

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Mar 19 2008 - 07:47:04 CDT

just the REMD ones, or none of them, or ?
if the test acses fail, please let us know more about
your system configuration- OS, compiler, MPI version, etc.
Also copy the exact error messages that sander gives.

On Wed, Mar 19, 2008 at 8:14 AM, Guillaume Renvez <grenvez_at_laas.fr> wrote:

> Hi,
> no, the test cases do not work.
>
> Carlos Simmerling wrote:
> > do the test cases for REMD work?
> >
> > On Tue, Mar 18, 2008 at 1:07 PM, Guillaume Renvez <grenvez_at_laas.fr
> > <mailto:grenvez_at_laas.fr>> wrote:
> >
> > yes, and it also occurs when I add it in the command line:
> > mpirun -np 4 sander.REM -O -rem 1 -remlog remd.log -ng 2 -groupfile
> > groupfile
> >
> > Carlos Simmerling wrote:
> > > this error occurs when you add -rem 1 to the groupfile?
> > >
> > > On Tue, Mar 18, 2008 at 12:21 PM, Guillaume Renvez
> > <grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>
> > > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>>> wrote:
> > >
> > > now I've got the correct syntax, it's working fine with the
> > > command line:
> > >
> > > mpirun -np 4 sander.REM -O -ng 2 -groupfile groupfile
> > >
> > > but if I add the flag '-rem 1', I still have the same error
> > > message. do
> > > you think it is a compilation error, or can it be something
> > else?
> > >
> > > Carlos Simmerling wrote:
> > > > you don't specify all of those things on the sander line,
> just
> > > the ng
> > > > and groupfile.
> > > > look at the test cases to see the proper syntax. see if that
> > > helps or not.
> > > >
> > > >
> > > > On Tue, Mar 18, 2008 at 10:09 AM, Guillaume Renvez
> > > <grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>
> > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>>
> > > > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>
> > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>>>> wrote:
> > > >
> > > > Hi Amber users,
> > > > when I launch my replica exchange calculation via the
> > command:
> > > > mpirun -np 4 sander.REM -O -ng 2 -rem 1 -remlog rem.log-i
> > > remd.in <http://remd.in> <http://remd.in>
> > > > <http://remd.in> -p
> > > > peptide.parm -c peptide.rst -o remd.out -x remd.mdcrd -r
> > > remd2.rst
> > > > -groupfile groupfile
> > > > where sander.REM is the executable which has been
> compiled
> > > with the
> > > > '-DREM' option, I got the error message :
> > > >
> > > > mdfil: Error unknown flag: -rem
> > > >
> > > > usage: sander [-O] -i mdin -o mdout -p prmtop -c
> > inpcrd
> > > -r restrt
> > > > [-ref refc -x mdcrd -v mdvel -e mden
> > -idip
> > > inpdip
> > > > -rdip rstdip -mdip mddip -inf mdinfo -radii radii]
> > > > Consult the manual for additional options.
> > > >
> > > > does anyone have an idea of what the problem is?
> > > >
> > > >
> > > > Guillaume
> > > >
> > >
> >
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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