(is there) a dependence of dynamics on WRAPPING

From: satya work (satya.work_at_gmail.com)
Date: Sat Aug 15 2009 - 01:33:26 CDT

Dear all,

I have a concern about wrapping in NAMD.

I have equilibrated a small protein-bilayer system for about 15 ns. After
this I ran two sets of simulations with exactlly the same initial conditions
except in one case WRAP was off and in the other WRAP on. I look at the RMSD
of protein to check that it has equilibrated etc.,

I ran 5ns in each case and was interested in calculating protein-lipid
contacts and I get quite different answers. May be this is because of the
Langevin piston (introducing random ness) used in the simulation, but still
I am concerned about this.. It is possible that my system has not
equilibrated yet, and this could be a problem of sampling.

Any suggestions?

Satya

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