Hi,
It would be better if you provided your input files so we can see
exactly what parameters you are using for each step.
On Sun, Feb 1, 2015 at 3:56 AM, Hadeer ELHabashy
<hadeer.elhabashi.gmail.com> wrote:
> Minimize only the water, restraining the protein (20000 cycles)
This is probably more than you need. Typically I will do about
1000/2000 steps depending on the system. The important thing is to
check your energies and gradient; you essentially want to see that
your energy vs step is "flattening out".
> Let water move (NTP, 300K), restraining the protein
How long did you run this for, and how strong were your restraints?
> Minimize water and protein (20000 cycles)
Again, probably too many steps here.
> Heat the system, restraining the protein (NVT 0 to 300K)
Why NVT here? Are you sure your density has equilibrated? If not you
run the risk of creating vacuum bubbles.
> Relax the system, restraining the protein heavy atoms (NPT, 300K,
> 0.5ns)
> Relaxthe system (NPT, 300K, 5ns)
You should look at your energies, temperature, density, etc and make
sure your system is actually coming to some sort of equilibration.
> However once I calculated the AMD parameters EthreshP, alphaP, EthreshD &
> alphaD as described in the manual and tried to run the last step of the
> production AMD, I faced an error of " vlimit exceeded " at the first 1000
> steps. I've decreased the time step from 0.002 to 0.001 ps and run again
> .this just postponed the error after the first 1000 steps to 1020 md steps.
> Any suggestions ?!!!
This suggests to me that A) your system is still not
well-equilibrated, B) your boost energies are too high, or C) a
combination of both. What do your energy terms look like? Are any of
them unusually high (or have '*******')?
If you can provide some more information we may be able to make more
detailed suggestions.
-Dan
>
> Best Regards
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Feb 01 2015 - 12:00:03 PST
