[AMBER] Solvate box

From: John S <s.john634.gmail.com>
Date: Fri, 28 Jan 2011 11:13:27 -0500

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)

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Received on Fri Jan 28 2011 - 08:30:06 PST
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