Re: [AMBER] help in box size determination

From: David A Case <>
Date: Mon, 20 Jul 2015 08:24:54 -0600

On Mon, Jul 20, 2015, Robin Jain wrote:

> I have prepared a input file using Addtobox command with cell size 20.83
> Ang (calculated as per system density). Now when i visualize this output
> pdb file in Molden to prepare CPMD input file, it show the box size 24 to
> 25 ang. On editing cell parameters to 20.83 ang. in molden , some solvent
> molecules came out from box and show bad periodic boundary condition,
> Therefore i am in confusion what is going wrong with me. Please help me in
> this regard.

This sounds like a molden issue, more than an Amber one. AddtoBox should
create a pdb file with the desired cell size (see the CRYST1 record in
its output file). It's not clear (to me) why molden thinks it is bigger,
or exactly what you are editing in molden to change it back to a smaller
value. You generally will need to minimize the energy of the system
created by AddtoBox before submitting it to another program like CPMD.

Maybe others on the list are more familiar with this workflow. It could be
that packmol is a better option for you.


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Received on Mon Jul 20 2015 - 07:30:02 PDT
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