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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
