From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jan 11 2006 - 19:52:10 CST
The cell basis vectors are a bit like the size of your cell. So in your
case, they would be approximately:
cellBasisVector1 46 0 0
cellBasisVector2 0 49 0
cellBasisVector3 0 0 50
(in other words, x2-x1, y2-y1, z2-z1 along the diagonal)
The PME options define the size of your grid. You should try to have
approximately 1 grid point per A^3. Therefore, define the numbers
(integers) close to the dimensions of your system. Also, I believe the
algorithm is most efficient if you use numbers that are multiples of 2,3,
and/or 5. (So here, I would say something like 50 50 and 50 maybe).
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Zhi Qi
Sent: Wednesday, January 11, 2006 2:14 PM
To: namd-l_at_ks.uiuc.edu; zqi_at_purdue.edu
Subject: namd-l: help-minimization and equilibration of Ubiquitin in a water
box
Dear VMD,
Sorry to give you trouble, I have some questions duing minimization and
equilibration of Ubiquitin in a water box:
In the conf. file:
(1)How to get the parameters in Periodic Boundary Conditions?
I mean, for cellBasisVector1, cellBasisVector1, and cellBasisVector1.
In the NAMD Tutorial, it said, we can use:
set everyone [atomselect top all]
measure minmax $everyone
measure center $everyone
for example, if I get
set everyone [atomselect top all]
measure minmax $everyone
{7.55800008774 5.92500019073 -8.70499992371}
{53.7410011292 54.7379989624 42.9179992676}
measure center $everyone
30.7318840027 30.3882675171 17.2441520691 ----for cellOrigin
Then,
# Periodic Boundary Conditions
cellBasisVector1 ? ? ?
cellBasisVector2 ? ? ?
cellBasisVector3 ? ? ?
cellOrigin 30.7318840027 30.3882675171 17.2441520691
(2)How to get the parameters in PME (for full-system periodic
electrostatics)?
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX ?
PMEGridSizeY ?
PMEGridSizeZ ?
Thank you very much!
Best Regards,
Zhi Qi
Physics Department
Purdue University
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