Atoms moving too fast with NAMD/Amber

From: Francesco Pietra (
Date: Thu Jul 26 2012 - 00:48:46 CDT

In connection with the suggestions below, is any general protocol to
follow when atoms move too fast with NAMD-CUDA when using Amber parm7
ff (prmtop/inpcrd)? It is implied that I am facing this problem after
succesful minimization and extreme care in settings for heating.

francesco pietra

On Thursday 06 May 2010 12:32:13 ipsita basu wrote:
> Thanks a lot for your reply. I tried timestep 1 before your reply and
> the job was running fine without giving any error. But the structure
> become distorted, it squeezes along z axis. Now according to your
> reply I am fix the langevin temp to zero and heating the system
> gradually by loop. This part is given below:
> # gradual temp increase
> run 1000
> for { set TEMP 0 } { $TEMP <= 290 } {incr TEMP 1 } {
> langevinTemp $TEMP
> run 1000
> I hope this will not disturb the structure.
> Any suggestion from your end would be appreciated.

Mmmmh, you probably should double check your structure.
I never ran into problems setting temperature, langevinTemp and
LangevinPistonTemp to 303 Kelvin from start.

Make sure to minimize your structure long enough.
At one point it could be necessary to tune the minimization parameters (in
case of bad contacts which are not removed during a normal minimization).
Once I was forced to use CHARMM with the SD minimizer to get my structure
minimized correctly (after this I could run the simulation in NAMD).

To preserve the structure of you protein you should apply constraints to the
protein backbone (C-Alphas, ~10 kcal/(mol*Angs^2)) and reduce them step by
step. Something like this:

constraints on
consref cons.pdb
conskfile cons.pdb
conskcol B
constraintScaling 1.0

# Minimization
minimize 2000
reinitvels $temp

run 20000
constraintScaling 0.5

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:18 CST