[gmx-users] Criteria and Energy Conservation

[David van der Spoel]

gtroiano at if.usp.br wrote:
>  Thank you very much again, David! Then it's fine for me, since what I want to
> do is a single point QM in "termalized" snapshots of the dynamics and not QM
> minimization.
But then you will get systematically incorrect energies due to weird 
(force field dependent) bond lengths etc.
> 
>  Gustavo
> 
>> gtroiano at if.usp.br wrote:
>>>  Dear GROMACS Users,
>>>
>>>  I'm trying to use GROMACS to get some MD snapshots for single-point
>> quantum
>>> mechanical calculations, trying to observe HOMO-LUMO gap of a protein
>> immersed
>>> in water with counterions, at a given salt concentration (4600 atoms in
>> total).
>>> I'd like to know if they are reliable enough to send to QM calculations.
>> I've
>>> got two questions: Which are the criteria I should be looking at? And one
>> of
>>> them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A
>>> cutoff for vdw and coulomb, with PME electrostatics, and double precision),
>> and
>>> the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but
>> I've
>>> got 0.3-0.5 in all simulations I've done. What should I do?
>>>
>> This is because of T coupling. If you turn off T coupling it will be
>> better (but you will not have constant T, and the energy will dirft in
>> the long run). Your starting structures are fine for QM, but QM
>> minimization will take a LONG time.
>>
>>
>>>  Thanks in advance,
>>>
>>>  Gustavo Troiano Feliciano
>>>
>>>
>>> ----------------------------------------------------------------
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>>
>> --
>> David van der Spoel, Ph.D.
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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