On 5/6/13 4:21 AM, gromacs query wrote:
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box (please correct me if wrong)
What you are seeing is a completely normal consequence of periodic boundary
conditions. You don't need to change the trajectory in any way to do density
measurements; the resulting values will be the same before and after centering,
since there is no "outside" or "center" of an infinite system.
-Justin
So by doing this:
trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc mol
-center
Select group for centering: I selected my polymer only
Select group for output: I selected all atoms (polymer + water + ions)
Please let me know is this correct way of modifying trajectory to calculate
water and ion density?
regards,
Jiom
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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