Re: [gmx-users] atoms not part of any of the T-coupling groups

Dear Justin Many thanks for this...all is now well. Best Garry On 24 Oct 2008, at 20:42, Justin A. Lemkul wrote: Wouldn't it be better to couple the Protein and Zn2+ together (i.e., index group Protein_Zn2+)? Coupling ions separately often leads to weird behavior/explosions when they're fre

Re: [gmx-users] atoms not part of any of the T-coupling groups

Wouldn't it be better to couple the Protein and Zn2+ together (i.e., index group Protein_Zn2+)? Coupling ions separately often leads to weird behavior/explosions when they're free in the solvent. I've never dealt with proteins that have ions bound, so I'm curious to see what everyone else thin

Re: [gmx-users] atoms not part of any of the T-coupling groups

Garry, I believe you are trying to not temperature couple the 4 zincs. To do this put the 4 zincs in one group and include that group in the listing of tc_grps and then correspondingly assign tau_t. tau_t=0 means no temperature coupling, but I think you will also need to give a temperature for the

Re: [gmx-users] atoms not part of any of the T-coupling groups

garry wrote: I am a novice at Gromacs (although I used Gromos 20+ years ago!)I have a dimer with two zincs per monomer, and I get the following complaint when running the grompp with pr.dmp, which I assume is referring to the 4 zincs. There are: 6789 OTHER residues There are:

[gmx-users] atoms not part of any of the T-coupling groups

I am a novice at Gromacs (although I used Gromos 20+ years ago!)I have a dimer with two zincs per monomer, and I get the following complaint when running the grompp with pr.dmp, which I assume is referring to the 4 zincs. There are: 6789 OTHER residues There are: 262PROT