AMBER Archive (2008)

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

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Tue Mar 18 2008 - 10:29:39 CDT

it did help! thanks

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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