From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Fri Dec 31 2010 - 02:29:43 CST
Hello NAMD Experts,
I am facing a problem running an NPT simulation of a protein in a lipid bilayer. After minimization, when I am trying to run an NPT simulation, I find that the simulation crashes giving the error message "Constraint Failure in The Rattle Algorithm For Atom 11181 (or may be some other number, which are in the lipid bilayer). I even tried to constrain the bilayer and equliibrate the solvents but it is of no help. Please help me in this regard.
Also,
there is a problem. In our clusters, if we submit a job with NAMD for more than 1 node, it does not use the 2nd and/or the other nodes. The nodes remain vacant/unoccupied by the respective job.
Can any one of you assist me?
with regards
Prathit Chatterjee
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