AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Mar 20 2008 - 09:47:32 CDT

maybe you can send me your config file directly (not to the whole amber
list).
something sounds like it didn't compile right. I'll have to look into it
since I haven't
used amber8 in a long time.

On Wed, Mar 19, 2008 at 9:57 AM, Guillaume Renvez <grenvez_at_laas.fr> wrote:

> yes, I compiled with both -DMPI and -DREM flags
>
> Carlos Simmerling wrote:
> > did you compile with both MPI and REM specified?
> >
> > for REMD I strongly suggest upgrading to more recent
> > Amber, such as 9 or perhaps 10 with it comes out. the REMD
> > implementation has improved significantly.
> >
> > On Wed, Mar 19, 2008 at 9:35 AM, Guillaume Renvez <grenvez_at_laas.fr
> > <mailto:grenvez_at_laas.fr>> wrote:
> >
> > 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>
> > > <mailto: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>>
> > > > <mailto: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>>>
> > > > > <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:
> > > > >
> > > > > 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>>>>
> > > > > > <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:
> > > > > >
> > > > > > 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>>>>>
> > > > > > > <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 <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>
> > > > > > > <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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