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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