VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Fri Dec 05 2014 - 15:33:06 CST

I pretty sure I can build the box, but I guess I'm really not sure why the
default settings generate a less dense water box. Is there something
special about this density of TIP3P water that makes it the default choice
for MD simulations? Some initial checks of some trajectories I ran
indicated I could scale the results of the less dense sims to get estimates
for water at 1 g/cc. But I don't understand why that would work.

Cheers,
--Jim

On Fri, Dec 5, 2014 at 8:58 AM, Richard Wood <Richard.Wood_at_purduecal.edu>
wrote:

> 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
>