Re: SMD simulation: stop applying force during simulation?

From: Axel Kohlmeyer (
Date: Fri Apr 08 2011 - 07:46:54 CDT

On Thu, Apr 7, 2011 at 11:05 PM, THANH NGUYEN <> wrote:
> Hi everyone.
> I'm doing a molecular dynamic simulation of a antigen antibody binding with
> a water box and there's some problems
> I intend to apply SMD force to the antigen for 200,000 timesteps (to give it
> a velocity), and then remove the force and observe how the antigen and
> antibody react for the remaining time (800,000 timesteps). The number of
> steps is 1,000,000 (one million).

> 2. Using 2 namd simulations:
> Simulation 1:
> "...SMD on
> <SMD force details>
> run 200000"
> then on Simulation 2:
> "...
> <use coor and vel file from first simulation as the initial coordinate and
> velocity for second simulation>
> ...
> SMD off
> run 800000"
> I have no error. The trajectory files show the antigen moving within first
> simulation, but stops within the second (stops moving and stays where it was
> at the end of 1st simulation, still fluctuating). Looks like the momentum
> from the first simulation was not carried on to the 2nd one.
> It would be greatly appreciated if someone could suggest me what to fix in
> this situation. Is there a simpler way to do this?

what is there to fix? you are moving a small object in a dense liquid.
have you ever tried to "throw" an object under water?

i would expect the dense liquid around the object to dissipate any
momentum very quickly.


> Thanks a lot.
> --
> Thanh Nguyen.
> It doesn't matter whether you are a lion or a gazelle.
> When the sun comes up, you better start running

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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