AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Mar 18 2008 - 09:29:38 CDT

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> 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 -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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