[AMBER] help

From: Robin Jain <robinjain.chem.gmail.com>
Date: Thu, 13 Nov 2014 11:29:24 +0530

Dear all,
 I want to simulate an organic molecule in methanol. Since i want to
simulate it in fix no. of methanol 80 and box size 17.58. For this i have
follow this process-

first i used *AddtoBox* command to simulte my sytem with fix no. of
solvent and then i go to *xleap* and used *setbox* command and then i used
*saveamberparm* command for *prmtop* and *inpcrd* file and finally i used
*chbox* command to get desired box dimension in inpcrd file and then i
manually edit prmtop file in FLAG_BOX_DIMENSIONS.

Now i want to know that have i done right or wrong and how could i manage
periodic boundary condition in that.
Robin Jain
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Received on Wed Nov 12 2014 - 22:00:02 PST
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