[gmx-users] how to know solvent molecule number

spss4 at iacs.res.in spss4 at iacs.res.in
Wed Apr 5 15:45:18 CEST 2017

  ----- Message from Chintan Bhagat <cbb.chintan at gmail.com> ---------
    Date: Wed, 5 Apr 2017 18:42:30 +0530
    From: Chintan Bhagat <cbb.chintan at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: [gmx-users] how to know solvent molecule number
      To: gromacs.org_gmx-users at maillist.sys.kth.se

> Hello,
> I want to do stimulation of my protein in solvent, ethanolamine
> 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?
> for reference please find attched files.
> Thanking you in advance.
> --
> Regards,
> Chintan Bhagat
> Research scholar,
> Veer Narmad South Gujarat University,India

I think you are doing some mistakes. 1AKI_processed.gro should contain 129
molecules and 1960 atoms as you are using 1AKI.pdb (your file contains SOL
also??). If you want to add a certain number of solvent then you can use
-cs -maxsol   command. If you want to add solvent randomly using -cs then
you can get number of solvents from 1AKI_sol.gro file and write the number
in topol.top file..

----- End message from Chintan Bhagat <cbb.chintan at gmail.com> -----

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