AMBER Archive (2007)

Subject: Re: AMBER: deeper problem with the energetics

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 17 2007 - 08:56:43 CDT

I see your charge sum is not zero- are there any force field parameters that
you added? that can also be a common source of shake failures.
otherwise it seems reasonable to me.

On 5/17/07, Pankaj R. Daga <pdaga_at_olemiss.edu> wrote:
>
> Hi Amber community,
>
> I am running a MD simulation with one homology model, I have built. For
> doing so, I have carried out four step minimization (Solvent, Hydrogen,
> Side-chain and Full), followed by two step heating (0-100 at constant
> volume, force const 20 and 100-300 at constant pressure, force const 10).
> Finally Three step equilibration each 100 ps at constant pressure with
> decreasing harmonic constraints (1, 0.1, and 0). All the precautions were
> taken to equilibrate the system properly.
>
> When I am running the last equilibration step, I ended up in the error
> saying that SHAKE cannot be accomplished. Here is the error as follows. I
> have searched through the archives, for the similar problem. I found that
> these problems are mostly associated with harmonic constraints. In my case,
> I don't have any. Still I am facing this problem.
>
> Can anybody suggest me, what the problem could be? I am attaching the
> input and output file along with.
>
> Please help.
>
> Regards
>
> Pankaj
>
>
> ===================================================================
> vlimit exceeded for step 32333 ; vmax = 82.6417035434410
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 3211 6561 6562
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> ===================================================================
>
>
> ===================================================================
> If your ship doesn't come in, swim out to it.......Jonathan Winters
> ===================================================================
> Pankaj R. Daga |
> Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
> 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
> University of Mississippi | phone: +1-662-915-1853
> University, MS, 38677-1848 |
> ===================================================================
>
>

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