Dear Amber user,
Our system contains only one molecule (that is peptide).
with regards,
Venkat
> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
M.V.Satish Kumar,
Research Scholar,
Department of Biotechnology,
IIT,
Guwahati-781 039
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Received on Mon Aug 25 2014 - 05:00:02 PDT
