[gmx-users] how to know solvent molecule number

[Justin Lemkul]

On 4/10/17 10:14 AM, Chintan Bhagat wrote:
> Dear Justin,
>
> As You advised, I tried grep -c option
>
> My solvent file - ethanolamine.gro
>  PRODRG COORDS
>    12
>     1DRG  OAC      1  -0.083   0.327   0.043
>     1DRG  HAE      2  -0.146   0.373  -0.019
>     1DRG  CAB      3  -0.074   0.188   0.009
>     1DRG  HAC      4  -0.172   0.143   0.025
>     1DRG  HAD      5  -0.037   0.178  -0.093
>     1DRG  CAA      6   0.022   0.117   0.105
>     1DRG  HAA      7   0.026   0.011   0.079
>     1DRG  HAB      8  -0.015   0.136   0.206
>     1DRG  NAD      9   0.158   0.174   0.097
>     1DRG  HAG     10   0.193   0.162   0.004
>     1DRG  HAH     11   0.217   0.125   0.161
>     1DRG  HAF     12   0.155   0.271   0.120
>    0.53926   0.53926   0.53926
>
> So, I tried OAC as unique atom to count the number of ethanolamine (solvent
> molecule) in my box.
>
> *lab1 at lab1-desktop:~/Desktop/md2$ grep -c OAC 1AKI_solv.gro10067*
>
> As i understand that my box is fully filled with 10067 ethanolamine
> molecules which indicate this will be stimulation in 100% ethanolamine (if
> I do further). If I want to do stimulation with 20% ethanolamine - 80%
> water. Then, number of ethanolmine should come around 2013 molecule
> (OAC=2013)  in 1AKI_solv.gro file.
>
> Is it correct?
>

Yes.

-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

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