[gmx-users] Virtual site and constraints

[David van der Spoel]

Нилов Дмитрий wrote:
> 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?

You can define it as zero, but take care to get the right moment of 
inertia (by defining further virtual sites).

> 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).
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se