help-minimization and equilibration of Ubiquitin in a water box

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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