[gmx-developers] implicit solvent in the git version of gromacs

[Mark Abraham]

----- Original Message -----
From: Carlo Camilloni <carlo.camilloni at gmail.com>
Date: Tuesday, June 1, 2010 19:43
Subject: [gmx-developers] implicit solvent in the git version of gromacs
To: gmx-developers at gromacs.org

> Dear Gromacs Developers,
> 
> I am trying  to test, without any success, the implicit 
> solvent algorithm implemented in the git version of gromacs.
> I am using a 16 residue beta-hairpin with the charmm forcefield 
> and all the different implicit algorithm still, ecc.
> But the system explode within the first steps, while turning-off 
> the gbsa all goes well.
> 
> pbc=no
> electrostatic=reaction-field-zero or cut-off
> vdw=shift or cut-off
> dt=0.002 or 0.001
> constraint=lincs
> nstlist=1
> rlist=rgblist=2
> both with temperature coupling as without.
> 
> Is the algorithm still broken?

That's hard to say without seeing a full .mdp file - you haven't mentioned more than one GB-relevant parameter there... I have got what resembled working GB from the attached .mdp, though obviously it's undocumented pre-release software and your mileage will vary... Berk fixed a minor bug today, so pull the git again.

Mark
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