[gmx-users] number of water molecule

[Alexander Alexander]

Thanks for your response.

The first layer of water molecules are in the within of 0.5 nm on top of
the solid surface(Other), and I try to  count the number of water
molecule(SOL) in this region as you suggested by gmx select, I used below
command but it gives me the total number of SOL molecules existing in the
whole box!

gmx select 'Close to Other' resname SOL and within 0.5 of group "Other"  -f
prd.gro -n input/index.ndx -os size.xvg

Available static index groups:
.
.
Group 16 "Other" (4096 atoms)
.
.
Group 21 "SOL" (8688 atoms)
.
.

Would you please let me know where I am doing wrong?
Thanks,
Alex


On Fri, Jul 15, 2016 at 6:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/15/16 10:19 AM, Alexander Alexander wrote:
>
>> Dear gromacs user,
>>
>> Just suppose a single amino acid is adsorbing to a solid surface in
>> aqueous
>> solutions. I was wondering how I can find out the number of water
>> molecules(immediate to the surface) that are washed away by amino acid in
>> such an adsorption?
>>
>>
> Count the number of waters in the first solvation layer using, e.g. gmx
> select.
>
> -Justin
>
> --
> ==================================================
>
> 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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