[gmx-users] constraints

[Nicola Staffolani]

OK, got it, thanks a lot Justin! ;) .0005 ps is indeed working...
It is not clear to me what I miss - from the Chemistry or Physics point of
view - when I constraint the X-H bonds... I mean, will the "rest of the
dynamics" (for example, the oscillations of the other couples of bonded
atoms) be affected if the H-X bonds are constrained, so that my results do
not make sense any more?

By the way, in my case where I am getting WARNINGs regarding N-H bonds,
constraints = h-bonds
looks to be a convenient way to fix the problem, if I do not want to make
dt smaller: is that advisable?


On Mon, May 12, 2014 at 3:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/12/14, 9:03 AM, Nicola Staffolani wrote:
>
>> Hi Justin,
>>
>> thank you for your clear reply!
>>
>> However, it still comes as surprising to me that a "standard" N-H bond
>> (entered as a gb_2 one with the same parameters as described in Table
>> 2.5.2.1 of the GROMOS96 Manual and User Guide) enters in conflict with the
>> standard dt value: indeed dt = 0.002 → tau < 5 · dt and dt = 0.001 → tau <
>> 10 · dt (where with tau I have meant the period associated to the harmonic
>> frequency) but dt = 0.001 is right the default
>> value<http://manual.gromacs.org/online/mdp_opt.html#pp>of dt! So it's
>>
>> like who constructed GROMACS didn't know that using the
>> default dt value and by just bonding a H atom to a N one would produce a
>> WARNING...  What am I missing?
>>
>> By the way, I have done an estimate of tau = 2 · pi · sqrt(µ/k), where µ =
>> m_H · m_N / (m_H + m_N) is the reduced mass of H and N and it looks right
>> what the WARNING is asserting...
>>
>>
> Beware - you can't equate "default" with "standard."  Indeed there are
> "default" values for most settings in the case that the user does not
> specify values. These should not be viewed as "standard" in any case.
>  Those of us who constructed Gromacs have tried to make life relatively
> simple for the user, but we can't think of every possible combination;
> there's just no way to do that from a software engineering perspective.
>
> If you are not using any constraints, you must adjust dt accordingly
> (0.0005 fs, probably).  Most applications will use constraints, as most
> force fields at least constraint X-H bonds nowadays, though the original
> parametrization may not have.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36