RE: help-minimization and equilibration of Ubiquitin in a water box

From: JC Gumbart (
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: [] On Behalf
Of Zhi Qi
Sent: Wednesday, January 11, 2006 2:14 PM
Subject: namd-l: help-minimization and equilibration of Ubiquitin in a water

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


# 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

# 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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