[gmx-users] cgnr in top file
gmx3 at hotmail.com
Mon May 3 16:34:45 CEST 2010
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
> 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.
> > 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
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