VMD-L Mailing List

From: S.K. Ghosh (skg30_at_cam.ac.uk)
Date: Mon Jun 23 2008 - 07:22:06 CDT

Hi VMD users,

I am creating a water box with just water in it. I am using the Solvate
Graphical User Interface to do that. Could you please clear a few
confusions that I am having.

1. I have ticked Waterbox Only and put in the Box Size Min and Max values.
Does Box Padding values play any role here? Is there a diff in density of
water filled in first with that padded in?

2. What's the density of water created by solvate plugin?

3. What does SegmentId prefix and Boundary stand for?

Your help will be much appreciated.

Thanks,
Sourav