From: Werner Crous (crous.werner_at_gmail.com)
Date: Tue Sep 15 2009 - 03:03:06 CDT
Dear all
I am new to NAMD and want to use a truncated octahedron water box. I
equilibrated a 110A truncated octahedron box in CHARMM within the NPT
ensemble, then solvated my protein and ligand, ran NPT to adjust the
volume of the box and then NVT for 500 ps. I then tried to run NVT
with langevin in NAMD with triclinic unit cell imaging based on the
vectors in the CHARMM output file. I used the following input for the
imaging and particle mesh ewald.
set a 92.42967
set p 109.471220634
set pi 3.14159265358979323
set cosp [expr cos($p * $pi/180)]
set sinp [expr sin($p * $pi/180)]
set Bx [expr $a*$cosp]
set By [expr $a*$sinp]
set Cx $Bx
set Cy [expr $a*$cosp*(1-$cosp)/$sinp]
set Cz [expr sqrt($a*$a - $Cx*$Cx - $Cy*$Cy)]
cellBasisVector1 $a 0 0
cellBasisVector2 $Bx $By 0
cellBasisVector3 $Cx $Cy $Cz
cellOrigin 0.0 0.0 0.0
PME yes
PMEInterpOrder 6 ;#interpolation for B-spline
PMEGridsizeX 100 ;#should be a combination of multiples of 2 and 3 (and 5)
PMEGridsizeY 100
PMEGridsizeZ 100
PMETolerance 1.69e-11
a is the side of the truncated octahedron as in my NPT simulation with CHARMM.
When I tried to run the simulation the energies were extremely high
and there were problems with the Settle algorithm. I then minimized it
for 100 steps with conjugate gradient and then I was able to run
dynamics. Unfortunately, the kinetic energy was extremely high giving
temperatures of nearly 1000K and this for a system which was
equilibrated or near equilibration in CHARMM.
Based on recent discussions on the list, it seems as if it is not
feasible to use truncated octahedron boxes in NAMD. I now want to
know, that if I want to run a simulation in NAMD should I rather try
to use a very large sphere or what do you suggest based on experience?
It seems as if the imaging might be the main problem. When I
visualized the box in vmd it looked as if it deformed significantly at
some corners almost immediately.
Thank you in anticipation
Werner Crous
PhD student
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