Re: Questions

From: Edward Patrick Obrien (
Date: Mon Jul 19 2004 - 17:02:29 CDT

Hi Manali,
  I think that these options may help your protein-out-of-the-box problem:

wrapAll on
wrapNearest on

You should avoid simulating waters you don't need, it just adds to the
computational cost.

In case you didn't know there is nothing wrong with your protein wandering
out of the box (I assume you are using Periodic boundary conditions), it
is just interacting with the image molecules. The physics is still the
same as if it was in the box.

I don't have an answer to the second part of your question,

On Mon, 19 Jul 2004, Manali Mehendale wrote:

> Hi,
> 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 ?
> Thanks,
> Manali

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