From: Zhi Qi (zqi_at_physics.purdue.edu)
Date: Wed Jan 11 2006 - 14:13:45 CST
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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