Re: [AMBER] Implicit solvation method: problem with the rst file

From: Jason Swails <>
Date: Mon, 25 Aug 2014 07:33:41 -0400

On Mon, 2014-08-25 at 16:38 +0530, M.Venkata Satish Kumar wrote:
> Dear Amber users,
> We have carried out implicit solvation method for the simulation of our
> system (peptide)containing 42 amino acids. Everything went fine upto the
> heating step. But in the equilibration step we faced the problem.
> We have problem with the rst file.
> The rst file contains ********. So the file is not able to read for the
> next step of simulation.

Are there multiple molecules in your system? If so, and they do not
remain stably bound for the duration of the simulation, then they will
drift apart ad infinitum and there is not much you can do about it
without restraining them to not separate by "too much". GB simulates an
"infinitely dilute" system, so it's not like the situation using PME
where molecules cannot drift that far away due to the periodic boundary
conditions, so this isn't an "imaging problem" like is reported for
explicit solvent simulations.

> Here is the equilibration input file:
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=100000, dt=0.002,
> ntc=2, ntf=2,
> ntt=1, tautp=0.5,
> tempi=325.0, temp0=325.0,
> ntpr=500, ntwx=500,
> ntb=0, igb=1,
> cut=999.,rgbmax=999.
> /

A few comments here. ntt=1 is a poor thermostat in general, and even
worse for GB. I would recommend ntt=3 instead.

Also, the igb=1 model is, I believe, the oldest GB model available, and
one of the poorest in terms of simulating proteins. I would recommend
igb=8 instead (with the mbondi3 radii) unless you have a very specific
reason for choosing what you did.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 25 2014 - 05:00:02 PDT
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