AMBER Archive (2008)

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

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Tue Mar 18 2008 - 12:07:54 CDT

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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> >
> >
>
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