[gmx-users] editonf: Center of Mass?

[Nicola Staffolani]

indeed it is now working with -center - sorry for not having tried it
before ;)

thank you very much Justin, helpful as always!!

Nicola


On Fri, May 30, 2014 at 2:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/30/14, 6:32 AM, Nicola Staffolani wrote:
>
>> Dear gmx community,
>>
>> I have a layer of Au atoms to which a molecule is attached. After pdb2gmx,
>> when I create the box and put H2O molecules inside using editconf, since
>> the planar dimensions of the Au layer are big compared to the
>> corresponding
>> dimensions of the molecule, I have decided that I want my box to be
>> triclinic.
>>
>> After that I give the box vector lengths a,b and c, I get that along the
>> direction perpendicular to the Au layer the box is shifted with respect to
>> the system (= Au layer + molecule). In order then to fully enclose the
>> system with H2O molecules, what I did is to make the box bigger, but this
>> costs time and I would like to understand what is happening and find a
>> proper solution.
>>
>> I have read the gmx online reference about editconf
>> <http://manual.gromacs.org/online/editconf.html>: where it is said that
>>
>> "Both -box and -d will center the system in the box", is the Center of
>> Mass
>> (CoM) meant?? This would make sense, since my shifted box is shifted
>> towards the Au layers, whose Au atoms are much heavier than the atoms of
>> the molecule. What I would like to achieve is to geometrically (and not
>> gravitationally) center the system inside my box, getting rid in this way
>> of the H2O molecules which are under the Au layers. Is there any smarter
>> way to use editconf to achieve that without resorting to manually
>> eliminating the unwanted H2O molecules?
>>
>>
> You can define whatever position you like with -center based on whatever
> box size is appropriate, rather than relying on -box and/or -d, if they are
> giving undesirable results.
>
> -Justin
>
>
>  ​For completeness of information, my executable water.com ​
>> ​file is:
>>
>> editconf -f speptide.gro -o -bt triclinic -box 7.2 5.4 6.4
>> genbox -cp out -cs   -p speptide -o speptideh
>> editconf -f speptideh     -o azwater.pdb
>>
>> Thank you in advance,
>>
>> Nicola​
>>
>>
> --
> ==================================================
>
> 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