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

[Alexander Alexander]

On Tue, Aug 2, 2016 at 10:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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...
>

Of course the most top layer has coordinate and geometry, you mean then I
can again define an index file with the most top atoms?
One way that I know but I do not like it is first calulate COM(peptide) to
COM(slab) and then subtract it by a constant which is half of the slab
thickness.  [COM(peptide)-COM(slab)] - [slab(thicjness)/2]. But I am
looking for a more straight one.

>
> 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
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