VMD-L Mailing List

From: mdcooper (mdcooper_at_uvic.ca)
Date: Fri Oct 08 2004 - 17:35:37 CDT

Hello,

another question ...

I see in the topology file that there is a H1 H2 bond required for Shake and,
I see from: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0233.html
that NAMD will ignore it if rigid bonds is on.

What I have done is built a solvent square and then, because of computational
necessity, I have shrunk the solvent box to "within 12 of protien" in VMD. I
then reran psfgen to get the psf file. When I loaded the psf file the water
molecules turned into pretty triangles.

Is this going to affect the MD simulation? Is there a better way of getting i
tighter solvent layer?

Thanks,

matt