[gmx-users] adding mix solvent

Nur Syafiqah Abdul Ghani pqah123 at gmail.com
Tue Sep 25 10:27:37 CEST 2012

Dear All,

I already produce my co-solvent topology file also with gro file.
Next step is i need to put the co-solvent first before i enter the
water molecule inside my box and mix them with the protein.
But right now i had a problem during put the co-solvent part.

I used this command : genbox -cp protein_box.gro -ci solv.gro -p
control.top -o protein_solv.gro

but then there was no any molecule of my co-solvent inside the box
with the protein.
Then i know i must have the itp file to include in the control topology.
But what i can do with the topology of the co-solvent?What is the
relationship between co-solvent.gro and
co-solvent.top which i  might can used both of them in my GROMACS simulation?

Four your infomation i used antechamber to produced my co-solvent topology.
Any advises from the pro one?

Thanks in advance!

Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
alternative email : syafiqahabdulghani at gmail.com

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