From: Axel Kohlmeyer (
Date: Tue Jan 20 2009 - 09:03:51 CST

On Tue, 20 Jan 2009, gurunath katagi wrote:

GK> Dear sir,
GK> i am new to the namd.
GK> i have performed the equilibriation of a protein molecule in a water box
GK> for 5ps. and now that i want to perform molecular dynamics simulations to
GK> observe the dynamics of the protein in the same condition for 5ps(after
GK> equilibriation).
GK> what will be the step or what parameters have to be manipulated in the
GK> configuaration file of equilinriation. and is it possible to combine these
GK> two thins in a single configuartion file ( i.e equlibriation followed by
GK> dynamics) and how?

please have a look at the NAMD tutorial and learn from them.

in general it is inconvenient to mix equilibration and production
run. an equilibration has to continue until the system is reasonably
equilibrated. how much of a trajectory is needed for that can be
hardly predicted and thus has to be monitored manually. it can change
from system to system. 5ps is most likely far from sufficient. have a
look at publications of MD studies of similar size systems that describe
the relevant simulation protocol.


GK> please reply
GK> yours sincerely
GK> Gurunath

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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