VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Fri Dec 05 2014 - 07:29:22 CST

Hello,
  I'm confused by choice of the initial conditions used to build the
standard water box generated by solvate 1.5.

Examining the .pdb and .psf files
/opt/lib/vmd-1.9.1/plugins/noarch/tcl/solvate1.5/wat.pdb and *.psf
that are used to generate the box, I find the box is cubic with side = 67.2
Angs and contains 9261 water molecules, which yields a density of 0.91 g/cc.

Searching this forum for explanations, I found
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2006-2007/3263.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2006-2007/3259.htmlhttp://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15968.html

Which indicate that there are some issues related to
a) parameterization of the TIP3P model, but that still indicates with "bad"
parameters, i.e. the standard ones, the density is 0.979 g/cc, which is
more than the default solvate box
b) the suggestion to "squeeze" the box after building (using NPT?) to
appropriate density has not significantly changed the volume of my
simulations after the initial few 100 ps of simulation time (I ran to 5
ns). I suppose I could increase the pressure to a few hundred bar to
improve the squeezing.

But I'm curious why this is necessary? Or more appropriately, why wasn't
the initial cube set with a higher density? I can generate my own cube,
and attempt to run psfgen and simulations, but these defaults have been in
place for much longer than my experience in MD sims and so I guessing there
is a good reason for these defaults and I'd like to avoid making silly
mistakes by just ignoring them.

Cheers,
--Jim

Department of Physics and Astronomy
The University of Texas at San Antonio