Re: [AMBER] Solute free non-water solvent

From: David A Case <>
Date: Tue, 14 May 2019 13:34:58 -0400

On Tue, May 14, 2019, razie yousefi wrote:
>I need to use AMBER for simulating a simple Argon gas system. What I
>have found on the web and tutorials, include bio-molecules inside water,
>for which AMBER is designed. I couldn’t find any thing related to solute
>free non water systems. Also, the input files are very huge and I have
>no idea about the specific commands I need to use to produce them for my
>system. Would you please help me get to know what to do? Thanks!

You should just be able to create a PDB-format file just containing
argon atoms in some initial conformation. Then, make a library file for
Ar that just has Lennard-Jones terms. (This will look like files for
monoatomic ions like NA or CL, except that the charge will be zero, and
the LJ parameters will be those appropriate for argon.)

Then give it a try...I expect this will be an educational experience:
it's especially uncertain how barostats designed for condensed phase
systems will work for a gas. But I've done liquid argon this way,
mapping out a part of the (known) equation of state, so working with a
gas might be straighforward.

I don't understand why your input files are "very huge". What kind of
files are these? How many atoms do you plan for your system? I'd
suggest starting our with a small number (as few as 1000) just to get
your feet wet and to make it easier to de-bug any problems that arise.

...good luck....dac

AMBER mailing list
Received on Tue May 14 2019 - 11:00:02 PDT
Custom Search