Re: [AMBER] help

From: David A Case <>
Date: Thu, 13 Nov 2014 06:57:42 -0500

On Thu, Nov 13, 2014, Robin Jain wrote:

> 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.

The above sounds fine. If you box is orthorhombic, the the command
"set <unit> box 17.58" (instead of setbox) should be easier. Then you
won't have to use ChBox or manually edit the prmtop file.

...good luck...dac

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Received on Thu Nov 13 2014 - 04:00:06 PST
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