Thank you very much, but in what way can I define the carbon
like massless when it treated as a virtual site(type 3)
in formate molecule?
Grompp runs with error when carbon has mass:
converting bonded parameters...
# CONNBONDS: 3
# CONSTR: 3
# VSITE3: 1
Setting particle type to V for virtual sites
ERROR 2 [file "fmt.top", line 82]:
virtual site C (Res FMT-1) has non-zero mass 12.011
-----------------------------------------------------
This is my topology:
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
FMT 3
[ atoms ]
; nr type resnr residue atom cgnr charge
1 opls_279 1 FMT H 1 0.22 1.008
2 opls_271 1 FMT C 1 0.58 12.011
3 opls_272 1 FMT O1 1 -0.9 15.9994
4 opls_272 1 FMT O2 1 -0.9 15.9994
[ bonds ]
; ai aj funct
1 2 1
2 3 1
2 4 1
[ constraints ]
; ai aj funct c0
1 3 2 0.19850
1 4 2 0.19850
3 4 2 0.22400
[ angles ]
; ai aj ak funct c0
1 2 3 1 ang_FMT_H_C_O1
1 2 4 1 ang_FMT_H_C_O2
3 2 4 1 ang_FMT_O1_C_O2
[ virtual_sites3 ]
; Dummy from funct a b
2 1 3 4 1 0.345 0.345
Dummy constants is computed as follows:
H
C
O O
a = b = [dist(HC)/2] / [cos(ang(CHO)) * dist(HO)] =
= 0.113/2 nm / [cos(34.37 deg) * 0.1985 nm] = 0.345
Best regards!
-------------
Nilov Dmitri
-----Original Message-----
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Date: Sat, 19 Jan 2008 10:33:50 +0100
Subject: Re: [gmx-users] Virtual site and constraints
>
> Нилов Дмитрий wrote:
> > Hello!
> > I would like to involve formate molecule (HCOO-)in my dynamics, but I have
> > the problem when I use virtual site (type 3fd)for it.
> >
> > When I run grompp for single formate molecule, it`s ok.
> > But after solvating in bath of solvent (tip3p) grompp runs with error:
>
> In this case you would be best off defining three constraints from
> H O1
> H O2
> O1 O2
> and define the carbon as a virtual site defined by the plane (check
> TIP4P topology).
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