Osman -
Two issues:
1) pmemd is basically a fast version of sander, that does a subset of the
total sander functionality. The command line to use is the same as sander,
and is thus documented in the sander section of the manual. The pmemd
section of the manual is more involved in specifying the differences between
pmemd and sander, if I remember correctly.
2) pmemd is built in a separate step from the rest of amber in amber 8.
This is a consequence mostly of pmemd being available for a different set of
platforms and optimizing a bit differently. Dave Case would have liked to
unify the build (and rightly so), but I was more concerned about messing
things up. SO to have pmemd available, you have to go to the
amber8/src/pmemd directory, read the README, invoke the configure script
that is there with arguments (given if you do a ./configure -help), and then
do a 'make install' in the pmemd directory (you will also need to do a
'rehash' afterward for the csh to pick up the new executable, and have
$AMBERHOME/exe in your path (hardwired, or with $AMBERHOME defined prior to
PATH def)). There is a little installation info in the amber 8 manual
(pmemd section), and more info in the amber8/src/pmemd/README file (some of
this is more than you need to know unless you are porting pmemd to a
currently unsupported platform).
Regards - Bob Duke
----- Original Message -----
From: "Osman Gani" <osman.gani.fagmed.uit.no>
To: <amber.scripps.edu>
Sent: Friday, July 23, 2004 1:09 PM
Subject: AMBER: pmemd.
> I want to run pmemd in AMBER8 on Redhat Linux.I don't see any command line
usage for that in the manual.When I invoke "pmemd" it doesn't get the
command.What could be the problem?May be I am asking a naive question.But I
have to do hurry to go.
> Thanks in advance.
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jul 23 2004 - 18:53:00 PDT
