On Wed, Apr 2, 2014 at 9:03 AM, Nitin Sharma <sharmanitin.nus.edu.sg> wrote:
> Dear Jason,
>
> Following your instructions I successfully managed to strip extra solvent
> molecules.
>
> However, I am having a doubt and hope you can clarify it . As far as I
> know in PBC the molecules lost from one side are gained from other end.
> Hence, the water molecules lost from one end due to movement while
> simulating will appear from other end. This should result in shuffling of
> water molecules surrounding the protein. Now, as I have stripped water
> molecules i.e. from 7150-13526 is there a possibility that some of them
> were taking part in interaction in one or more trajectories?
>
The "strip" command will delete the atoms and all of their periodic images
from the system. From the look of your command, you are deleting about
half of your water molecules (!!) which will cause huge pockets of vacuum
in your system.
I'm not sure what you mean by "is there a possibility that some of them
were taking part in interaction in one or more trajectories?" -- every
particle interacts with every other particle in molecular simulations. By
deleting particles you are certainly getting rid of particles that _were_
interacting with other particles during the trajectory and creating
unphysical vacuum pockets in the system. I'm still puzzled about why
you're trying to match up the numbers of waters between two systems. If
you need to carry out any energy calculations, though, the system from
which you deleted ~6400 water molecules will be basically useless.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 02 2014 - 07:00:08 PDT
