AMBER Archive (2008)

Subject: AMBER: Deleting solute from box

From: Kevin Davies (kevinwdavies_at_gmail.com)
Date: Thu Feb 07 2008 - 14:45:48 CST

I'm trying to determine the solvated volume of a molecule via a
two-part calculation: minimization of the solute in an octahedral
water box, followed by minimization of the system without the solute
(i.e. just the water molecules).

I've completed the first calculation to my satisfaction, but am having
a problem setting up the second one (water only). Can anyone suggest
a way to remove the solute so I can run MD on the water alone? I
suspect this is easy, but everything I've tried has caused errors
(lost the periodic boundaries, etc.)

Thanks,
Kevin Davies
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