Dear Amber Users,
I made a solvate box using packmol with solvated polymer at center of box
saved it as pdb file
Then used xleap to make the box for the solvated polymer .
x=loadpdb pm_sol.pdb
set box x vdw 5
I used constant volume minimization and then constant pressure dynamics for
100 ps to equilibrate the box.Though this gives me no error,
when I visualize my trajectory in VMD , here the box size is much larger
and the contents are at the middle of the box .
Should I continue with the constant pressure dynamics to have the box size
same as contents of the box , or equilibrate it till it attains the usual
density of the solvent at room temperature (as 1g/cc for water)
Thanks
John
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Received on Fri Jan 28 2011 - 08:30:06 PST
