[gmx-users] How to solvate particular regions in simulation box

[Venkat Reddy]

Dear all,
I am trying to simulate virus hollow capsid using gromos54a7 forcefield.
Since the capsid is hollow, I don't want water inside the capsid. But the
"gmx solvate" command solvates the hollow region of capsid also. So, every
time I manually remove the water  located inside the capsid as follows.

1) I find the com of protein using gmx traj -f -s -com -ox
2) Using VMD, I extract out all the water molecules with in 'r' of capsid.
3) I proceed to energy minimization, equillibration, and final dynamics.

But the above mentioned process is not always fruitful, particularly when
the system is very big. Hence, I would like to know whether is there any
trick to solvate only certain regions (solvate only the regions which are
at 'r' distance from the com of protein) in the simulation box?

Thanks and regards

With best wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036