[gmx-users] how to know solvent molecule number

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 5 15:43:20 CEST 2017


gmx solvate reports on the terminal what it has done, doesn't it? Someone
needs to update the topology, so we wouldn't suppress the number you need


On Wed, Apr 5, 2017 at 3:13 PM Chintan Bhagat <cbb.chintan at gmail.com> 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?
> for reference please find attched files.
> Thanking you in advance.
> --
> Regards,
> Chintan Bhagat
> Research scholar,
> Veer Narmad South Gujarat University,
> India
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