[gmx-users] peptide's COM distance to top of a slab

[Justin Lemkul]

On 8/2/16 4:46 PM, Alexander Alexander wrote:
> Thanks Mark.
> I do not know what do you mean with the geometric criterion, but, It is a
> slab/vacuum model in which vacuum is in the Z direction normal to the slab.
> I am just interested in vertical distance between peptide COM and top most
> atom.
>

Rephrasing Mark's question: "how do you define the topmost atom?"  Then it 
becomes simple to do.  You have coordinates, therefore a geometry...

> One more question is that how I can calculate the distance between the two
> termini of a peptide versas time?
>

As you would the COM distance between any other species.  Create an index file 
with the first and last residue as separate groups.

-Justin

> Thanks,
> Alex
>
> On Tue, Aug 2, 2016 at 10:35 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> What's a geometric criterion that expresses "top of the slab?"
>>
>> Mark
>>
>> On Tue, Aug 2, 2016 at 10:22 PM Alexander Alexander <
>> alexanderwien2k at gmail.com> wrote:
>>
>>> Dear gromacs user,
>>>
>>> I have peptide getting adsorbed into a solid surface, I can get the
>>> distance between COM of peptide and COM of the slab by below command,
>>>
>>> gmx distance -n index.ndx -select 'com of group Other plus com of group
>>> Protein' -f noPBC.xtc -s prd.tpr -oxyz disxyz.xvg -tu ns
>>>
>>> I was wondering if a similar command is available to get the distance
>>> between peptide's COM and top of the slab?
>>>
>>> Regards,
>>> Alex
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================