[gmx-users] how to know solvent molecule number

[Chintan Bhagat]

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?

Thanking You
Chintan

On Wed, Apr 5, 2017 at 7:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/5/17 9:12 AM, Chintan Bhagat wrote:
>
>> Hello,
>>
>> I want to do stimulation of my protein in solvent, ethanolamine (different
>> percentage).
>> I have made box of 1 nm and then using command
>> "gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
>> topol.top",
>> As per my knowledge, i solvated my protein in ethanolamine.
>> Now I want to know the number of ethanolamine molecule present in box.
>> Then
>> I looked in to *.top* file but no information is availble in the file
>> (SOL).
>> (As per intruction, program is only hard-coded to update the topology in
>> the case of water).
>> I found increase in number of molecules from 7200 to 128004 in
>> /home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
>> respectively. It means something is inserted in box (must be
>> ethanolamine!!!!!-my guess)
>> How can i know number of ethanolamine molecules?
>>
>>
> Use grep -c with a unique atom name to count the number of any given
> molecule in the system.
>
>
>> for reference please find attched files.
>>
>>
> The mailing list does not accept attachments.
>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
India