Re: problem with installing NAMD in Linux Red Hat

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Mar 05 2012 - 08:57:35 CST

On Mon, Mar 5, 2012 at 9:24 AM, rukman kesh <ruk_s1987_at_yahoo.com> wrote:

>
> Is it necessary to install PVM before installing NAMD?
>

hell no! PVM is dead for over a decade and good riddance.

> VMD andCHARMM forcefield is needed. How to integrate all these things.
>

VMD is not needed, but very useful.

why don't you start with working your way through the NAMD
beginner's tutorial and properly read the documentation.
that is what it is for.

axel.

> --- 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
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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