AMBER Archive (2008)

Subject: AMBER: restarting molecular dynamics

From: Germain Vallverdu (
Date: Wed May 28 2008 - 08:18:16 CDT

Hello Amber

I would like to know exactly what append when I restart a molecular
dynamics with sander.

here is an example of my input file, I use AMBER 9 on a Linux system.
This is a simulation of an organic molecule in a TIP3P water box.

 nstlim=50000, dt=0.001,
 irest=1, ntx=5,
 ntpr=100, ntwr=100, ntwx=0,
 tempi=300.0, temp0=300.0, ntt=1,
 ntb=2, pres0=1.0, ntp=1, taup=2.0,
 ntc=2, ntf=2,

My problem is the following. I would like to do a simulation of about 10
ps step by step with a restart every 5fs. But if I compare the one step
run with the dashed run, trajectory are not similar after few steps.
Then I would like to know what exactly append when Sander starts.

I suppose that :
 - when sander start it computes the PME grids
 - if I use algorithm control of the temperature like Langevin or
Andersen perhaps there is a repeat of the random number chain because of
the seed is the same for every run.
 - the accuracy of the coordinate and velocities is better in the
program than in restrt files. Then this might lead to difference between

Nevertheless do you think that something like that is possible to do and
does it exist other process at the beginning of sander ?

Best wishes


Germain Vallverdu
Laboratoire de Chimie Physique
Université Paris Sud 11
01 69 15 30 38 / 06 88 59 08 87
/Chacun de nous a son étoile. Suivons la en nous félicitant de la voir 
chaque jour un peu plus loin !/ (V. Grignard)
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