RE: AMBER: I need some constant pressure MD help

From: Ross Walker <>
Date: Tue, 30 Jan 2007 21:47:38 -0800

Dear David,

> to see what's going wrong, but getting information out of a
> code that only
> does PME-based non-bonded forces for periodic systems and
> applying it to a
> code that currently works on periodic systems but does not
> yet include
> Ewald is painful.

If you want to turn off the ewald calculation and use a simple atom based
cutoff you can add the following to your input file:

  use_pme=0, eedmeth=4,

This is a simple atom based truncation scheme, there is no switching
function etc. It was removed from the Amber 9 manual as it really is not
recommended for periodic simulations. However, you may find it useful for

> 1.) What are the formats of the information in the "-o mdout"
> file? They
> seem pretty self-explanatory, except for:
> PRESSURE: kilopascals?

I'm not sure on this, perhaps other can comment. With regards to units in
general. Temperatures are in Kelvin, time typically in ps. All energies are
in KCal/mol and all forces in kcal/mol/A.

> 2.) I tried a case where I created a 216-water system in an
> appropriate
> periodic box. Using a 9A cutoff, I noted that the VDWAALS energy I
> obtained differed from AMBER's by about 1% (I'm not ready to compare
> electrostatics in periodic systems yet).

This is probably due to the long range contiuum model correction to the VDW
term to account for VDW interactions beyond the cutoff. Set vdwmeth=0 in the
ewald namelist to turn this off.

For comparing VDW et I would start with just two water molecules in a
suitably big box. That way you can print all the atom-atom interactions and
make sure you are matching properly. Once you have this you can scale up to
large more complex systems.

I'll let others comment on the specifics of the virial calculation as I am
not completely sure how this is implemented.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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Received on Wed Jan 31 2007 - 06:07:48 PST
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