[gmx-users] Constraints & Restraints

[Darrell Koskinen]

Thanks for the additional comments.

So given that, in my system, I have H atoms attached to C atoms on the perimeter of a finite graphene sheet that is placed above multiple infinite layers of graphene (graphite), would it be more appropriate to use: (i) a classical (harmonic) model using constraints=none or (ii) a constrained model using constraints=all-bonds?

Note that, currently, I use constraints=none and see that the C atoms in the graphene sheet are well behaved and not vibrating very much, but the H atoms on the perimeter are vibrating wildly. Would you have any idea of whether this is natural and to be expected or not? Maybe this is an indication that constraints should be used in this particular model. However, I have no idea whether it is natural for hydrogen atoms to flip and flop around so much on the edge of a graphene sheet. 

Your comments are appreciated.

Darrell

Date: Thu, 12 Nov 2009 14:16:06 +0100
From: Ran Friedman <r.friedman at bioc.uzh.ch>
Subject: Re: [gmx-users] Constraints & Restraints
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4AFC0A96.302 at bioc.uzh.ch>
Content-Type: text/plain; charset=ISO-8859-1

Erik Marklund wrote:

> > Mark Abraham skrev:
>   
>> >> Darrell Koskinen wrote:
>>     
>>> >>> Hi Tsjerk,
>>> >>> So then, if I understand correctly, setting "constraints =
>>> >>> all-bonds" is not as realistic as setting "constraints = none",
>>> >>> since the latter will allow for flexible (e.g. harmonic) behavoir
>>> >>> which is more realistic than fixing the bond to a certain distance,
>>> >>> correct?
>>>       
>> >>
>> >> Actually not. It would be a better model of a harmonic potential
>> >> (duh), but it has been shown that the use of constraints can lead to
>> >> a (more?) acceptable model of a real system, and they allow a larger
>> >> integration time to boot. Check out the papers for the constraint
>> >> algorithms (refs in GROMACS manual).
>> >>
>> >> Mark
>> >>
>>     
> > Agreed. And this is especially true for hydrogen atoms as I understand
> > it, since their behaviour as quantum particles deviate more from a
> > classical treatment than is the case for heavier nuclei. This is
> > mentioned in the gromacs manual.
> >
> > /Erik
>   
This depends on the system you study. In some cases it is necessary not
to constrain the hydrogen atoms to get a better agreement with the
experiment. Also,  if one needs to deal with vibrational spectra
involving hydrogens, they must be mobile.

Ran.

>>>> >>>> Date: Wed, 11 Nov 2009 21:45:44 +0100
>>>> >>>> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>>>> >>>> Subject: Re: [gmx-users] Constraints & Restraints
>>>> >>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>> >>>> Message-ID:
>>>> >>>>     <8ff898150911111245u63c6aa65sa839f246343521f4 at mail.gmail.com>
>>>> >>>> Content-Type: text/plain; charset=ISO-8859-1
>>>> >>>>
>>>> >>>> Hi Darrell,
>>>> >>>>
>>>> >>>> Constraints and restraints also apply to relative positions. A bond
>>>> >>>> constraint fixes the bond to a certain distance. constraints =
>>>> >>>> all-bonds means that all bonds are to be converted to constraints,
>>>> >>>> rather than have them flexible, e.g. harmonic. Harmonic bonds are
>>>> >>>> actually more like restraints, penalizing deviations from the
>>>> >>>> equilibrium values. These equilibrium values and the 'penalty
>>>> >>>> function' are described in the force field.
>>>> >>>>
>>>> >>>> Hope it helps,
>>>> >>>>
>>>> >>>> Tsjerk
>>>> >>>>
>>>> >>>> On Wed, Nov 11, 2009 at 9:32 PM,  <darrellk at ece.ubc.ca> wrote:
>>>> >>>>  
>>>>         
>>>>> >>>>> Hi,
>>>>> >>>>> I just have a quick question on contraints and restraints. My
>>>>> >>>>> understanding is that "constraints" fix the position of an atom in
>>>>> >>>>> space and "restraints" restrain the deviation of the atom's position
>>>>> >>>>> from its equilibrium point. Is that correct? If so, then I am a
>>>>> >>>>> little
>>>>> >>>>> confused by the purpose of "constraints = all-bonds" or "constraints
>>>>> >>>>> = none" in an mdp file, since by selection of a force field, which
>>>>> >>>>> has
>>>>> >>>>> bond/angle/dihedral stretching/bending/torsion constants, we are
>>>>> >>>>> specifying the constraints applied to the simulation. So then what is
>>>>> >>>>> the purpose of "constraints = all-bonds" and "constraints = none"?
>>>>> >>>>>
>>>>> >>>>> Thanks.
>>>>> >>>>>
>>>>> >>>>> Darrell
>>>>> >>>>>     
>>>>>           
> >
> >
>   


-- ------------------------------------------------------ Ran Friedman 
Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) 
Department of Biochemistry University of Zurich Winterthurerstrasse 190 
CH-8057 Zurich, Switzerland Tel. +41-44-6355559 Email: 
r.friedman at bioc.unizh.ch Skype: ran.friedman 
------------------------------------------------------