[gmx-users] how to know solvent molecule number

[Mark Abraham]

Hi,

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
;-)

Mark

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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