[gmx-users] Half double pair list method in GROMACS

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Sep 3 02:58:30 CEST 2011

I think it's reasonable for you to post this on-list. It's not your  
method and you got help here and somebody else might want the same  
help in the future.


-- original message --

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Sep 1 22:22:27 CEST 2011

     * Previous message: [gmx-users] pdb2gmx response time
     * Next message: [gmx-users] order parameter
     * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]


Thank you for your confirmation. I did the changes. I am currently  
doing some tests, I will send you a feedback about the results  
off-list (if you want) shortly.

A bientôt


Message: 1
Date: Thu, 01 Sep 2011 14:38:53 -0400
From: chris.neale at utoronto.ca
Subject: [gmx-users] Half double pair list method in GROMACS
To: gmx-users at gromacs.org
Message-ID: <20110901143853.537ln0dj94w4wc4c at webmail.utoronto.ca>
Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";

It's a typo, but it's in the discussion and not in the "do this" part
of the method so I decided not to mention it. I don't see another
question in this post, so I hope that you have figured things out.
Note that I have never tested the exact implementation that I
suggested in that April email. It seems like it should work just fine,
but it is numerically different than the OPLS/Berger combination so
there is no way to be sure until you check the energies as I
suggested. I'd be interested to have you report back on the energy
matching once you have done the tests.

Good luck,

-- original message --

Hi Chris,

Sorry to repost the same question, but I have really tested your method the
last few weeks. My question about the gen-pairs directive come from the fact
that I have read a message from you


Where you detailed how to use the Berger and OPLS force fields together in
the same system. By reading carefully the meaning of the gen-pairs
directive, I found several errors in my force field.

BYW in your previous message


In the step 3, I think there is a typo, it is "values/10" instead of
"values/12". Am I right?

Thank you again


More information about the gromacs.org_gmx-users mailing list