Error in running tutorial files

From: Ragothaman Yennamalli (
Date: Wed May 18 2005 - 12:20:50 CDT

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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