AMBER Archive (2008)

Subject: AMBER: replica exchange : problem with sander

From: Guillaume Renvez (
Date: Tue Mar 18 2008 - 09:09:34 CDT

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 -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?

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