AMBER Archive (2008)

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

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Wed Mar 19 2008 - 08:35:55 CDT

I'm actually using the version 8 of Amber. the test cases I'm using are
those in the folder $AMBERHOME/test/rem.

Carlos Simmerling wrote:
> 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
> <mailto: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>
> > <mailto: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>>
> > > <mailto: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>>>
> > > > <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:
> > > >
> > > > 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>>>>
> > > > > <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 <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>
> > > > > <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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