RE: AMBER: Deep energetics problem

From: Ross Walker <>
Date: Tue, 2 Jan 2007 11:12:53 -0800

Dear Vikram,
This could be from a number of issues although the most likely is the
restraint force. 1000 KCal/mol/A2 is far too strong. What this will do is
induce very high frequency oscillations in the CA atom which are too fast
for the 2 fs step of your integrator and hence the system blows up. Do you
really need to keep CA of residue 1 fixed this tightly? Try something
smaller like 50.0 or so. Even this is large but it should work.
You might also have issues with your system not being minimised /
equilibrated properly. How well equilibrated were things from the run from
which you are restarting this?
I would start by just reducing the restraint force and see how you do. Note,
you may want to set nstlim to say 1000 and ntwx/ntpr=1 so that you get a
short run with every frame recorded. Then you can watch what happens to the
system. You may also want to reduce the timestep to say 1fs or so to ensure
better stability.
All the best

|\oss Walker

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From: [] On Behalf Of
sai vikram
Sent: Tuesday, January 02, 2007 09:10
Subject: AMBER: Deep energetics problem


I am trying to do a NPT simulation with a protein structure restraining

Restrain 2 to 20 residues


Restrain the CA atom of first residue strongly


Before this particular run i carried out a minimization amd Simulated
annealing step with restrains.
 RES 2 20
 Restrain the CA atom of first residue strongly

I wish my system should be at constant pressure 200.0 .



vlimit exceeded for step 6; vmax = 59.1247

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 78 140 141

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


I have tried to search in google and read the messages posted previously
by others, and reduced the restraints as per their suggestions. Yet, i could
not able to run my system

$ Can someone please advice me here. below is my input file
Input file is
  imin = 0, ntx = 7, irest = 1,
  ntpr = 100, ntwx = 500, ntwe = 0, ntwprt=0,
  ntc = 2, ntf = 2,
  nstlim = 50000, dt =0.002,
  tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
  ntb = 2, ntp = 1,taup=0.2, pres0=200.0,
 Restrain the heavy atoms
 RES 2 20
 Restrain the CA atom of first residue strongly
 * CA * *
 RES 1

Amber Version : 9

Operating System : Linux


Thanks in advance,


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Received on Wed Jan 03 2007 - 06:07:27 PST
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