VMD-L Mailing List

From: Richard Wood (Richard.Wood_at_purduecal.edu)
Date: Fri Dec 05 2014 - 08:58:47 CST

One could use CHARMm to build a water box having the correct density. I've done so in the past.

Richard

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Jim Parker [jimparker96313_at_gmail.com]
Sent: Friday, December 05, 2014 7:29 AM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Density of water box in solvate 1.5 plugin ~ 0.9 g/cc

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--_000_2795F52A14F49842BB6FF8003810E47D056A5E97PUCEX5staffpucp_--