RE: Error in running tutorial files

From: Pijush Ghosh (
Date: Wed May 18 2005 - 13:55:31 CDT

Hello Ragothaman
    This is a very common problem one faces in NAMD, fist thing I would like
to suggest you is, check the dimensions of your ubiquitin molecule in VMD or
by some other means, then in your configuration file see that the periodic
box size you have used are same or couple of Angs. bigger than those. Now
make your PME grid size also same as those dimension (at the same time see
those values are multiple of 2,3 or 5). Another suggestion is while doing
SMD start with smaller magnitude of force in that way you can make sure that
your system is not turning unstable because of very high K.E.
    Hope this helps.

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA

-----Original Message-----
From: [] On Behalf
Of Ragothaman Yennamalli
Sent: Wednesday, May 18, 2005 12:21 PM
Subject: namd-l: Error in running tutorial files

Hi all,

I am new to NAMD. I am learning SMD and when I tried
running SMD using the ubiquitin example, I got the
following error:

FATAL ERROR: Periodic cell has become too small for
original patch grid!
Possible solutions are to restart from a recent
increase margin, or disable useFlexibleCell for liquid

I searched the mailing list but they all are
suggesting to have a water sphere around the protein,
but the tutorial says without water sphere. The SMDDir
is the same as given in the tutorial.

Thanks in advance,



Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586

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