[gmx-users] number of water molecule

[Justin Lemkul]

On 7/15/16 6:37 PM, Alexander Alexander wrote:
> 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
>

That command isn't even syntactically valid and probably should have returned a 
fatal error; if you want help on setting up proper commands, you need to provide 
the exact command you used, copied and pasted.

Let's say your water O are named OW and the surface has a z-coordinate of 2.0 
nm.  Your command would look something like this:

gmx select -f prd.gro -s prd.tpr -n in.ndx -os size.xvg -select 'name OW and z < 
2.5'

I of course haven't tested that, but it should be something simple like that. 
See gmx help selections for additional help and examples.

-Justin

> 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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>> Gromacs Users mailing list
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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

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