Re[2]: [gmx-users] Virtual site and constraints

[Нилов Дмитрий]

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 <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at 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).