[gmx-users] cgnr in top file

[Berk Hess]

Hi,

This is not a decision, but a limitation of the grompp code.
I have fixed this in the git release.

Simply editing the charge group numbers by hand to make them all different
should work.

Berk

> Date: Mon, 3 May 2010 10:22:54 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] cgnr in top file
> 
> 
> 
> Erik Marklund wrote:
> > True. I guess gromacs groups together the terminal hydrogens, overriding 
> > the original force field parameters. Can't say why that decision was 
> > made, but it will influence your simulation very little.
> 
> I think there was a bug report some time ago involving virtual sites on the 
> termini of all-atom force fields causing a crash when the terminus crossed a 
> periodic boundary.  Could be related to that, although I can't remember the 
> exact progress behind the fix.
> 
> -Justin
> 
> > 
> > Erik
> > 
> > leila karami skrev:
> >> Dear Erik
> >>  
> >> you said Amber03 was not parameterized with charge groups and last 
> >> column in your rtp entry holds the chargegroup numbers. but
> >> cgnr column in my top file does not looks just like it. in case of H1, 
> >> H2 and H3.
> >>  
> >> /     H1    amber99_17   0.16420     2
> >> //     H2    amber99_17   0.16420     3
> >> //     H3    amber99_17   0.16420     4
> >> //    // /. that's ok. but why
> >>  
> >> /and my top file is as follow :
> >> //  //                                                        //    
> >> nr       type          resnr  residue  atom   cgnr   charge     mass  
> >> //      //2 amber99_17      1   NGLY     H1      2     0.1642      
> >> 1.008  //      3 amber99_17      1   NGLY     H2      2     
> >> 0.1642      1.008  //      4 amber99_17      1   NGLY     H3      
> >> 2     0.1642      1.008   //   /
> >> thanks for your attention        
> > 
> > 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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