[gmx-users] Problem after tranferred CHARMM c36 to Gromacs
mark.abraham at anu.edu.au
Sat Sep 4 01:05:24 CEST 2010
----- Original Message -----
From: Jianhui Tian <jianhuitian at gmail.com>
Date: Saturday, September 4, 2010 2:30
Subject: [gmx-users] Problem after tranferred CHARMM c36 to Gromacs
To: gmx-users at gromacs.org
> Previously in gromacs, if you use Ryckaert-Bellemans type dihedrals, you must erase the 1-4 pairs. Now for 4.5-beta3 dihedral function type 9, how do you deal with the 1-4 pairs? Thanks.
The need to manage 1-4 pairs and exclusions is independent of the function type used to implement the dihedrals, but rather depends on force field settings. You will need to compare what NAMD is doing with the forcefield documentation and reproduce that with GROMACS.
> ---------- Forwarded message ----------
> From: Jianhui Tian <jianhuitian at gmail.com>
> Date: Fri, Sep 3, 2010 at 10:17 AM
> Subject: Problem after tranferred CHARMM c36 to Gromacs
> To: gmx-users at gromacs.org
> Dear GMX users,
> I am interested in using CHARMM c36 force field in Gromacs. I wrote a script to generate the ffcharmmbon.itp, ffcharmmnb.itp and molecule.itp file.
> After that, I compared the energy terms from Gromacs and NAMD. The bond, angle, dihedral, improper and electrostatic energy terms all agree well.
> However, there are big difference for VDW energy terms. Does anyone have any hint for what might be wrong? Thanks a lot.
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