SMD simulation: stop applying force during simulation?

From: THANH NGUYEN (ncthanh1986_at_gmail.com)
Date: Thu Apr 07 2011 - 22:05:35 CDT

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).

I tried 2 scenarios:

1. Using 1 namd simulation:
"....
SMD on
<SMD force details>
run 200000

SMD off
run 800000
..."

this exhibits error after 200,000 timesteps ! This is easy to understand as
I reckon NAMD does not support SMD on and off with a single simulation so 2
tried the second scenarios:

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?

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

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