Re: Using NAMD for Metropolis Monte Carlo conformational searches

From: Axel Kohlmeyer (
Date: Wed Nov 10 2010 - 09:10:02 CST

dear ajasja,

On Wed, Nov 10, 2010 at 5:04 AM, Ajasja Ljubetič
<> wrote:
>> dear ajasja,
>> this kind of thing could in principle be done,
>> but i suspect you would need to change the
>> source code.
> Well, I suspect I will have to compile NAMD on windows sooner or later :)

why would you want to subject yourself to such a pain??

overall it continuously puzzles me, how much effort people
are willing to invest to be able to keep using windows,
even though the typical workflow in scientific computing
applications is so much easier to manage on a unix-like

> But I just remembered the IMD protocol. Perhaps it could be misused for this
> purpose? It is possible to get the energies back and perhaps using
> the IMD_FCOORD or IMD_MDCOMM header it is possible to send new
> conformations.

no. right now the IMD protocol is very limited. it should in principle
be possible to send coordinates (but there are no provisions to
send the cell information, for example), but that would have to be
implemented, and on top of that, you would have to do more changes,
since after sending the coordinates, you will have to initialize the
patch grid and neighbor lists, since you would not know if you can
re-use the previous ones.

as i wrote before your best options, in my opinion, are either
to use a code that is easier to modify or use one of those
MD toolkit script packages. since you are running on windows,
i assume that you are not handling a very large problem, so
performance really should not be an issue.

> Is there an IMD protokol specification somewhere? I have been reading the
> example source code found on the "main" IMD site as well as the NAMD source,
> but it takes longer to get an overview.

that code _is_ the specification. ;)


> Best regards,
> Ajasja

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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