Re: [AMBER] help

From: Robin Jain <>
Date: Mon, 17 Nov 2014 23:00:41 +0530

 My question is that my box is cubic and i want to maintain periodic
boundary condition also then am i going in right way or not.

On Thu, Nov 13, 2014 at 11:29 AM, Robin Jain <>

> 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

Robin Jain
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Received on Mon Nov 17 2014 - 10:00:02 PST
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