From: Wolbach, Jeffrey P \(WOLBACH\) (WOLBACH_at_juniata.edu)
Date: Mon Jun 13 2005 - 11:36:11 CDT
Yes, it is possible to make the Solvate plug-in read a different pdb file as the solvent template. You will have to edit the Solvate Tcl script, as I don't see any way to enter parameters of this nature on the command line call to Solvate. At minimum, one must change the lines initially referring to wat.psf & wat.pdb to instead refer to your lower-density water box, and also modify the line that starts "set watsize .... " to reflect the size of your lower-density water box. That should be all you need to do once you have generated your new water box. I would suggest first copying solvate.tcl to solvate.base or the like, then you can just swap filename extensions when/if you want to run with a "standard" density water box, rather than having to re-edit the Tcl code.
To generate the new water box, I found it to be simplest to choose the density, assume that the waters will be in a 3-D periodic lattice, and back calculate the separation of the O-atoms. That way one can start with a central H2O and replicate it in space by adding +(-)nX, +(-)nY, +(-)nZ to the coordinates of the original H2O to create the 3-D lattice. Probably the only trick is that I think one should end the box on a "half-interval" (i.e., build a 10 X 10 X 10 lattice, then add 1/2 delta X in each dimension to size the box).
I have used this procedure to make the Solvate plug-in work for generating systems that are solvated in DMSO instead of water. It was not entirely automatic, but the problems I encountered (related to having to check multiple heavy atoms in the solvent, instead of just a single O) should not occur if the solvent remains H2O. Worst-case scenario is that you have to execute a couple of Tcl commands in VMD. No big deal.
Von Leibig Researcher
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Leonardo Sepulveda Durán
Sent: Sunday, June 12, 2005 10:52 PM
Subject: namd-l: Adjusting Density of waterbox used by solvate
I would like to perform NVE or NVT dynamics in NAMD, to prove which is the influence of water density in my protein. I have used NPT, and I have found that, altrough average presure is well mantained, it fluctuates a lot, and volume too. I Thought a good way to adjust it is to solvate the system with a waterbox that has a desired water density from the begining. About such posibility, I would like to ask some
1) it is posible to say solvate plugin of vmd to use a diferent pdb for initial coordinates of water which have a desired density, or use a diferent script to allow for it,
2) if 1) is posible, does someone knows if there is a place where waterboxes of diferent density are available to be dowloaded? or maybe namd have it and I haven't found them??
Thanks a lot
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