RE: Continuing simulation after constraint failure error?

From: Sadhu, Shubho (NIH/NCI) [F] (sadhusj_at_mail.nih.gov)
Date: Thu Aug 06 2009 - 14:23:06 CDT

Try turning off rigidBonds.

Shubho
________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Sujata Sovani [sujatas_at_scripps.edu]
Sent: Thursday, August 06, 2009 12:59 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Continuing simulation after constraint failure error?

Hi All,

I did minimization and equilibration for 10000 steps fro a 377 residue protein. But I got the error
Constraint failure in RATTLE algorithm for atom 3327!
ERROR: Constraint failure; simulation has become unstable.

I got this for not only atom 3327 but may others, one of the solution given to this problem in the mailing list is to run the minimization longer.
There could be many other things that could have gone wrong but I want to know that if I want to continue minimization for more steps say 100000 can it be done from the current step (so as to save that much computational time). I am not sure if this is recommended (stuck in a local minima??) but if it is how to change the .conf file to restart the minimization from here??

Thank you.

Regards,
Sujata

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