Hi David,
Thanks for your response. Yes, I do have nitrogen molecules in my system
which is non-standard residues. So do you think if the cut-off distance may
also be the reason for that error?
Any further your idea/ opinion is highly appreciated.
Thanks again.
Best Regards,
Vu T.
Message: 2
Date: Thu, 8 Oct 2015 14:37:33 -0700
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] "Vlimit exceeded for step..." error
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20151008213733.GE10524.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Thu, Oct 08, 2015, Vu Truong wrote:
>
> I have a question about the "Vilmit exceeded for step.." error that showed
> in my output file. Please be noted that it still runs till the end of
> simulation time. I wonder if we can accept that simulation results. Or we
> have to fix the problems out. I have tried to read most of the archives
> message related to this error. And I have tested several ways likely
> reducing the time step, doing more relaxing minimization or so. It turns
> out for me that I can run it but they still showed this error for some
> steps in my output file.
If you only get the error occasionally, it may be ignored. But it probably
indicates that something is odd with your simuation, or that you are pushing
the limits of the integrator. Are there non-standard things in your
simulation (non-standard residues or ligands? high temperature? something
else odd in your selection of cutoffs, simulation parameters, etc.) If you
run what we call "standard" simulations (protein in water, using default
force fields and settings), a vlimit error should be very rare.
....dac
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Received on Fri Oct 09 2015 - 12:30:04 PDT
