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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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