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

2011-12-03 Thread ABEL Stephane 175950
-- Message: 1 Date: Fri, 02 Dec 2011 16:07:19 -0500 From: Chris Neale chris.ne...@utoronto.ca Subject: [gmx-users] Half double pair list method in GROMACS [update] To: gmx-users@gromacs.org Message-ID: 4ed93e07.5070...@utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; format=flowed What

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

2011-12-02 Thread Sai Kumar Ramadugu
Stéphane Message: 1 Date: Thu, 01 Sep 2011 14:38:53 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Half double pair list method in GROMACS To: gmx-users@gromacs.org Message-ID: 20110901143853.537ln0dj94w4w...@webmail.utoronto.ca Content

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

2011-12-02 Thread Chris Neale
off-list (if you want) shortly. A bientôt Stéphane 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

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

2011-09-05 Thread ABEL Stephane 175950
: Thu, 01 Sep 2011 14:38:53 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Half double pair list method in GROMACS To: gmx-users@gromacs.org Message-ID: 20110901143853.537ln0dj94w4w...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed

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

2011-09-02 Thread chris . neale
(if you want) shortly. A bientôt Stéphane 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

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

2011-09-01 Thread intra\sa175950
Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly

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

2011-09-01 Thread chris . neale
Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the

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

2011-09-01 Thread intra\sa175950
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 http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Where you detailed how

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

2011-09-01 Thread chris . neale
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

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

2011-09-01 Thread ABEL Stephane 175950
: chris.ne...@utoronto.ca Subject: [gmx-users] Half double pair list method in GROMACS To: gmx-users@gromacs.org Message-ID: 20110901143853.537ln0dj94w4w...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed It's a typo, but it's in the discussion