Re: Problem running REMD simulation

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Tue Aug 25 2015 - 04:16:55 CDT

Hi Nicholus,

Are you using a NAMD build based on a patched MPI build of Charm++? I
had to compile NAMD from source (by following the instructions in the
notes.txt file).

Alternatively there is a version on the NAMD download page called
"Linux-x86_64-netlrts (Multi-copy algorithms)" which might be what you
want (although it's hard to tell).

cheers,
Doug

Quoting Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com> on
Tue, 25 Aug 2015 10:01:36 +0200:

> Hello,
>
> I am reposting the query as I have not got any reply.
>
> I am trying to run REMD simulation using NAMD. I am following the
> suggestions given in
>
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node66.html
>
> I did the following
>
> example$ mkdir output
> example$ cd output
> output$ mkdir 0 1 2 3 4 5 6 7
> output$ cd ..
> example$ mpirun /usr/local/NAMD_2.9_Linux-x86_64-multicore/namd2 +replicas
> 8 job0.conf +stdout output/%d/job0.%d.log
>
> I got the error message
> %%%%%%%%%%%%%%%%%%%%%%%%%%%
> FATAL ERROR: Unknown command-line option +replicas
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Unknown command-line option +replicas
>
> Charm++ fatal error:
> FATAL ERROR: Unknown command-line option +replicas
> %%%%%%%%%%%%%%%%%%%%%%%%%%
>
> The second part of the question is about running REMD using AMBER topology
> file.
> For running normal simulation we change in the configuration file
> "structure XXX.psf" by
> amber yes
> parmfile XXX.top"
>
> Now in REMD configuration file what we change for the following line
>
> set psf_file "XXX.psf"
>

_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston

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