AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Mar 18 2008 - 12:12:03 CDT

do the test cases for REMD work?

On Tue, Mar 18, 2008 at 1:07 PM, Guillaume Renvez <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>> 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>>> 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> -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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