I think you need to know how much of this difference is normal run to run
variation before you assign it to the buffer size.
On Apr 9, 2011 11:21 AM, "Sangita Kachhap" <sangita.imtech.res.in> wrote:
Hi all
I am studying water mediated protein-DNA interaction.
I have done different trails to acihive this.
I have solvated system with TIP3P 6 Angstrom, 8 Angastrom and 12 Angstrom
from the
surface of system.
When I visualized the trajectory and and H-Bond analysis for the mask atom
with
solvent.
For
6 Angstrom - occupancy of H-Bond between mask and solvent is 8.9% of tatal
11ns
run.
8 Angstrom - occupancy of H-Bond is 19% of total 11ns run.
12 Angstrom - occupancy of H-Bond is 70% of total 4ns run.
Here I am cofuse how to decide upto what distance I should add TIP3P to
system.
Here can anybudy please giude me.
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Apr 09 2011 - 10:00:02 PDT
