On Apr 13, 2011, at 7:07 PM, Sasha Buzko wrote:
> Bud, Jason,
> thank you for your suggestions. I did run initial minimizations before
> any further heating/density equilibration, although not with the
> multistage minimization and heating, as mentioned by Bud. Will
> experiment with it now.
>
> Best,
>
> Sasha
>
Did you set the box to give you the experimental density? If the
box was larger than that, you may not have a problem.
The symptoms I am talking about typically arise when you use the
packmol home web page density estimator to estimate the box size for
a final density at that temp, then try to go immediately to those
conditions.
The symptom is sander dropping core after only a few steps of
minimization. If you can do more than 10 steps of minimization without
the program crashing, you should be OK to just start equilibration
(in my experience, at least).
Bud
ps, for the archives: the problem is at the edges of the box. Since
the packmol solvent cell is not relaxed to the force field, when the
boxes are stacked immediately adjacent to one another, you have vdw
overlaps. The short minimizations are to just move the solvent
molecules a little bit to eliminate solvent vdw overlaps big enough
to give energies large enough to cause floating point overflow.
Alternatively, create the system with buffer volumes between the
simulation cells (lower density than experimental), then squeeze out
the voids with NPT dynamics (this is a more leap-like approach).
>
> Jason Swails wrote:
>> On Wed, Apr 13, 2011 at 4:33 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>>
>>
>>> Thanks, Jason.
>>> Manual addition of the box flag resolved the previous issue, but pmemd
>>> complained about the lack of ATOMS_PER_MOLECULE records in the prmtop
>>>
>>>
>>
>> Ah, I didn't realize that your prmtop file didn't have ATOMS_PER_MOLECULE.
>> That's certainly necessary. Wrapping/imaging is done based on that, as well
>> as pressure scaling. I would suggest following Bud Dodson's advice, as I
>> believe he has a bit of experience with packmol --> amber (you can check the
>> archive for his contributions to that effect!). My comments/suggestions are
>> borne completely out of my experience with the sander code and topology file
>> formats, not any practical hands-on experience with packmol (even though
>> I've suggested it as a tool in the past ;) ).
>>
>> All the best,
>> Jason
>>
>> file. So I just reran tleap with setbox command, and everything was
>>
>>> taken care of. Only needed to manually correct the solvent start index
>>> to make sure that both octanol and water are treated as solvent.
>>>
>>> Thanks again for your help
>>>
>>> Sasha
>>>
>>>
>>
>>
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--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
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Received on Wed Apr 13 2011 - 19:00:03 PDT
