Re: problem with installing NAMD in Linux Red Hat

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Mar 05 2012 - 08:33:01 CST

NAMD takes input when it runs, you can specify in the input file which
CHARMM forcefield you are using, you should read through the manual, it's
extremely well documented, and also maybe try some of the basic tutorials.

2012/3/5 rukman kesh <ruk_s1987_at_yahoo.com>

>
> Is it necessary to install PVM before installing NAMD?
> VMD andCHARMM forcefield is needed. How to integrate all these things.
> --- On *Mon, 5/3/12, Andreas Förster <docandreas_at_gmail.com>* wrote:
>
>
> From: Andreas Förster <docandreas_at_gmail.com>
>
> Subject: Re: namd-l: problem with installing NAMD in Linux Red Hat
> To: "rukman kesh" <ruk_s1987_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Date: Monday, 5 March, 2012, 2:50 PM
>
>
> Dear Rukman,
>
> with something as plain vanilla as RH 32-bit, why don't you just
> download the binary, unpack and use? It's the third on the list of the
> Version 2.8 (2011-05-31) Platforms, NAMD download page. If you do have
> multiple cores on your single processor, you should instead download the
> multicore binary (fifth item on the list).
>
> Hope that helps.
>
>
> Andreas
>
>
>
> On 05/03/2012 7:39, rukman kesh wrote:
> >
> > Hello Sir,
> >
> > I'm using 32 bit Red Hat platform and single processor. Steps I'm using
> > for installation are:
> >
> > **
> >
> > * /mkdir NAMD/
> > * /cd NAMD/
> >
> >
> >
> >
> >
> > Unpack NAMD and matching Charm++ source code and enter directory:
> >
> > * /tar xzf NAMD_2.8b1_Source.tar.gz/
> > * /cd NAMD_2.8b1_Source/
> > * /tar xf charm-6.3.0.tar/
> > * /cd charm-6.3.0/
> >
> >
> >
> > *Source Compilation-*
> >
> >
> > Build and test the Charm++/Converse library (network version):
> >
> > * /./build charm++ net-linux-x86_64 --no-build-shared
> --with-production/
> >
> > I'm having problem at the above mentioned step. Error is compilation
> > failed with gcc...
> >
> > please provide me with useful information for installing NAMD on Linux.
> >
> >
> >
> > * /cd net-linux-x86_64/tests/charm++/megatest/
> > * /make pgm/
> > * /./charmrun ++local +p4 ./pgm /
> > * /cd ../../../../../
> >
> >
> > --- On *Thu, 1/3/12, Chris Harrison /<charris5_at_gmail.com<http://mc/compose?to=charris5@gmail.com>>/*
> wrote:
> >
> >
> > From: Chris Harrison <charris5_at_gmail.com<http://mc/compose?to=charris5@gmail.com>
> >
> > Subject: Re: namd-l: problem with installing NAMD in Linux Red Hat
> > To: "rukman kesh" <ruk_s1987_at_yahoo.com<http://mc/compose?to=ruk_s1987@yahoo.com>
> >
> > Cc: namd-l_at_ks.uiuc.edu <http://mc/compose?to=namd-l@ks.uiuc.edu>
> > Date: Thursday, 1 March, 2012, 11:47 AM
> >
> > Rukmankesh,
> >
> > In order for us to help you, please provide much more specific
> > information that details very clearly step-by-step what you did to
> > install NAMD, and what you experienced/saw/etc.
> >
> > Best,
> > Chris
> >
> >
> >
> > On Wed, Feb 29, 2012 at 12:40 AM, rukman kesh <ruk_s1987_at_yahoo.com<http://mc/compose?to=ruk_s1987@yahoo.com>
> > </mc/compose?to=ruk_s1987_at_yahoo.com<http://mc/compose?to=ruk_s1987@yahoo.com>>>
> wrote:
> >
> > Hello,
> >
> > I am having problem in installing NAMD in Linux Red hat having
> > xeon single processor. Please someone help me with installation
> > instructions and various modules to use.
> >
> > Rukmankesh
> >
> >
> >
> >
> > --
> > Chris Harrison, Ph.D.
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Theoretical and Computational Biophysics Group
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> >
> > http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> > http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar> Fax:
> > 217-244-6078
> >
> >
> >
>
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
> http://www.msf.bio.ic.ac.uk
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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