From: Manali Mehendale (
Date: Mon Jul 19 2004 - 14:08:10 CDT

  I am trying to perform an MD simulation of a protein which has 750
residues. I solvated it using VMD keeping a water thickness of 10
angstrom. The resulting system becomes very big ~ 95,000 atoms. The
simulation is fine till 2ns. After 2 ns of simulation the protein comes
out of the waterbox but program doesnt complain (I have tried restarting
the simulation numerous times after 2ns to see if protein moves in instead
of out).
Is there anyway i can control the translational motion of the protein ?
I do use the wrapall ON (which someone suggested on the mailing list).
One option was to increase the size of waterbox, i have rebuilt the
system with 15 angstrom thickness and between the 3rd and 4th ns the
protein is almost at the edge of the waterbox!
 (The protein has a triangular shape)
I dont want to go on increasing water box size for longer simulation
time, the system is already very big !
Please help me with this.
  I was also interested in looking at individual velocities of each atom
(if that has any bearing on the translational move out of the box), the
way i tried doing this is by the following :
 set all [atomselect top all]
 set fil [open velocity.dat w]
 foreach x [$all get x] y [$all get y] z [$all get z] {
  puts $fil "[expr sqrt( pow($x,2) + pow ($y, 2) + pow ($z, 2) )]"
 close $fil
 Is this the right way to get the magnitude of the individual velocities
? I was also wondering if the units would be Angstrom/ fs ? Also the range
for normal and abnormal velocoties ?


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