AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Mar 19 2008 - 08:25:11 CDT

something is not right about that, this is not text that amber9 should
write.
please confirm which Amber version you are using for the executable
and which version of the test cases you are using.

On Wed, Mar 19, 2008 at 9:13 AM, Guillaume Renvez <grenvez_at_laas.fr> wrote:

> juste the REMD tests crash with the same 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.
>
> I run these tests on a Altix 3700 server administrated by a Linux (64
> bit) system and the intel ifort compiler was used.
>
> Carlos Simmerling wrote:
> > just the REMD ones, or none of them, or ?
> > if the test acses fail, please let us know more about
> > your system configuration- OS, compiler, MPI version, etc.
> > Also copy the exact error messages that sander gives.
> >
> >
> > On Wed, Mar 19, 2008 at 8:14 AM, Guillaume Renvez <grenvez_at_laas.fr
> > <mailto:grenvez_at_laas.fr>> wrote:
> >
> > Hi,
> > no, the test cases do not work.
> >
> > Carlos Simmerling wrote:
> > > do the test cases for REMD work?
> > >
> > > On Tue, Mar 18, 2008 at 1:07 PM, Guillaume Renvez
> > <grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>
> > > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>>> wrote:
> > >
> > > 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>
> > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>>
> > > > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>
> > <mailto: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>>
> > > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>
> > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>>>
> > > > > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>
> > <mailto:grenvez_at_laas.fr <mailto:grenvez_at_laas.fr>>
> > > <mailto: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> <
> 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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