AMBER Archive (2007)

Subject: RE: AMBER: vlimit exceeded, polarizable force field

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Nov 29 2007 - 10:02:24 CST

>From page 94 of the amber 9 manual:
 
The time step (psec). Recommended MAXIMUM is .002 if SHAKE is used, or .001
if it isn’t. Note that for temperatures above 300K, the step size should be
reduced since greater temperatures mean increased velocities and longer
distance traveled between each force evaluation, which can lead to
anomalously high energies and system blowup. Default 0.001.
 
If you don't know what the concept of a timestep is then you need to go to
the library and get yourself some books on molecular simulation and the
concept of integrating Newton's equations of motion.
 
Note in terms of affect for a system at equilibrium running a shorter
timestep will give you better integration of the equations of motion and in
theory a more 'precise' trajectory. In practice below some threshold one
typically does not see much of a difference - at least over a few ps or so.
2fs is probably bleeding edge for shake simulations, 1.5fs can be better in
some cases, less than this is probably just overkill and uses more cpu time
for a given simulation length. Without shake you need 1.0fs or less. For
highly strained systems, or bad initial structures (such as from homology
modelling) you may need to run initial relaxation runs with a shorter time
step until the system relaxes away from the initial bad state.
 
Good luck.
Ross

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Denis Courtier
Sent: Thursday, November 29, 2007 05:33
To: amber_at_scripps.edu
Subject: Re: AMBER: vlimit exceeded, polarizable force field

I have decrease dt value. I am running at two values. One as dt=0.0002 and
another as dt=0.001. Both are running.

Does anybody know how dt affects to my calculation? Thank you.

Denis.

On Nov 29, 2007 11:43 AM, Denis Courtier <amber982_at_gmail.com> wrote:

Hello everybody.

I am trying to run a polarizable force field, ff02pol.r1.

But, I got an error. Now, it is in md step. The error in my output file is:

vlimit exceeded for step 5; vmax = 36.3511
vlimit exceeded for step 6; vmax = **********

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 9 8 9

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

My input files, for minimization and md, are:

Initial min-n
 &cntrl
  ipol=1
  imin=1, maxcyc=2500, ncyc=1000,
  cut=8.0, ntb=1,ntc=2,ntf=2
/
  and

300K constant temp MD
 &cntrl
  ipol=1
  imin=0, ntb=1
  cut=8.0, ntc=2, ntf=2,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=1.0,
  nstlim=520000, dt=0.002,
  ntpr=50, ntwx=50,
 /

Can anybody help me? How can i control vlimit? Where is the origin of my
problem? Does i have to change the ensemble?

Thank you in advance.

Denis.

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