AMBER Archive (2008)

Subject: RE: AMBER: big molecule numbers ( simulation with many formamide molecules )

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Jul 26 2008 - 08:58:34 CDT

Hi Adrien,

 

You can't directly define the number of molecules of formamide that
solvatebox adds, just the buffer. However, it is fairly simple to write a
quick shell script that runs tleap and refines the buffer size to the
solvatebox command to give you the number of formamide molecules that you
require.

 

If you want to see the formamide box after you solvated your solute just
'edit' the unit in xleap. Alternatively save your prmtop and inpcrd files
and then look at them in something like VMD. The tutorials on the amber
website show you how to do this.

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Adrien Delmont
Sent: Saturday, July 26, 2008 2:04 AM
To: amber_at_scripps.edu
Subject: AMBER: big molecule numbers ( simulation with many formamide
molecules )

 

Dear All,

 

Thanks a lot for your suggestions. I want to run a simulation with many
formamide molecules. Well but How can I define the molecule number for a
'solvent' box containing lots of my own molecules. And Are there any
different options for running a simulation with many formamide molecule ?
also I want to see the simulation box and my formamide molecules in it. So
How can I do that?

 

Many thanks in advance

 

Adrien

 

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