[gmx-users] Density as a function of time

[Ashutosh Akshay Shah]

Thanks a ton Justin :)

On Tue, Feb 16, 2016 at 12:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/16/16 12:22 PM, Ashutosh Akshay Shah wrote:
>
>> Hello Gromacs Users,
>>
>> I want to find the number of ions in a specific part (say left half) of
>> the
>> cell as a function of time.
>>
>> gmx density gives me a time average value across the box (cell), and I
>> know
>> that I can manually find the density for small time steps(0-1,1-2 ns...)
>> and plot the values obtained for the left half of the cell as a function
>> of
>> time, but it would be much easier to do the same with a single command.
>>
>> Any suggestions?
>>
>>
> Use gmx select to find the number of ions that satisfy whatever geometric
> criteria you like.
>
> -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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