AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Mar 18 2008 - 11:39:01 CDT

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> 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>> 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> -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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