[gmx-users] number of water molecule

[Alexander Alexander]

Hi,

Sure, but choosing oxygen atom also give the TOTAL number of O atom in the
whole BOX which is not what I want but I want the number of O atom which
are closer than 0.5 nm to the surface.
I also tried your another suggestion below(I hope right usage), but nothing
new, again total number of Oxygen in the box.

gmx select 'water O atom with z < 0.5 + Other_z_value' -f prd.gro -s
prd.tpr -n in.ndx -os size.xvg

Even reducing the 0.5 to 0.00005 also give the same number of Oxygen.

Cheers,
Alex


On Fri, Jul 15, 2016 at 10:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/15/16 3:11 PM, Alexander Alexander wrote:
>
>> 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
>>
>>
> This will give you the total number of atoms in the selection.  Select by
> the oxygen atom name to count the number of waters.
>
> Even more simply, you can define a coordinate value for the selection
> instead. If the surface is in the x-y plane, select any water O atom with z
> < (0.5 + surface_z_value).
>
> -Justin
>
>
> 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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> --
> ==================================================
>
> 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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