VMD-L Mailing List

From: Bogdan Costescu (Bogdan.Costescu_at_IWR.Uni-Heidelberg.De)
Date: Fri Apr 22 2005 - 08:09:11 CDT

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On Thu, 21 Apr 2005, Kos wrote:

> The problem is that when we analyze large 1ns .dcd file the X-VMD
> dissapears/crashes and can't read.

Most probably the trajectories are too large to load in memory (RAM).
Either split the trajectories in smaller pieces or get a computer with
larger memory (eventually a 64bit capable one).

> Is CHARMM an alternative solution to these problems and can treat
> large files faster because doesn't need graphics?

A bit simplified view is that CHARMM might not need much memory for
analysis because it can load the trajectory frame by frame, so at any
given time only one frame is in memory. The disadvantage is that it
makes the analysis limited by the I/O bandwidth of the computer (to
local disk or NFS server) when you want to do several passes through
the whole trajectory; if you load the whole trajectory in RAM, it's
much faster for the second or subsequent passes.

> A general question: Is CHARMM a more advanced package for MD
> analysis although not so friendly and how does compare in the
> postprocessing part with VMD?

Such a general question can't be answered properly. You should visit:

http://www.charmm.org

where you can find documentation and a forum with many active posters.
Then make a comparison based on _your_ needs. 

-- 
Bogdan Costescu
IWR - Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen
Universitaet Heidelberg, INF 368, D-69120 Heidelberg, GERMANY
Telephone: +49 6221 54 8869, Telefax: +49 6221 54 8868
E-mail: Bogdan.Costescu_at_IWR.Uni-Heidelberg.De