Virutal particles should not have any mass.
Its, e.g. for placing a delocalized charge (as in TIP4P) somewhere.
How about carefully reading the warnings and try to do, what they suggest?
How about this?:
> 5 opls_966 1 FMT D 1 12.011 0.0
Now you have a charge there and no mass. Thats, how virtual sites work.
If you want to use a "free energy dummy", you may have to use a
different approach.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Нилов Дмитрий wrote:
I`ve tried to name it like atom (instead of "dummy mass")
in this way:
1)enter new atom type in "ffoplsaa.atp":
opls_966 12.01100 ; Virtual site in formate
2)enter description of new atom type in "ffoplsaanb.itp":
; name bond_type mass charge ptype sigma epsilon
opls_966 DF 0 12.011 0.0000 D 0.00e+00 0.00e+00
(also I`ve tried to use "A" instead of "D" in ptype column)
3)correct my topology:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_279 1 FMT H 1 0.22 1.008
2 opls_271 1 FMT C 1 0.58 0.000
3 opls_272 1 FMT O1 1 -0.9 15.9994
4 opls_272 1 FMT O2 1 -0.9 15.9994
5 opls_966 1 FMT D 1 0.0 12.011
[ constraints ]
; ai aj funct c0
1 3 2 0.19850
1 4 2 0.19850
3 4 2 0.22400
[ virtual_sites3 ]
; Dummy from funct a b
2 1 3 4 1 0.345 0.345
5 1 3 4 1 0.345 0.345
But it does not work because grompp runs with error
"virtual site D (Res FMT-1) has non-zero mass 12.011".
I suppose, that only "dummy masses"(particles named like "M*") could
have mass.
Could you help me, please?
--------------------
Nilov Dmitri
-----Original Message-----
Нилов Дмитрий wrote:
OK, could I add "dummy mass" that has coordinates and
mass such as carbon to keep right moment of inertia?
I mean something like this:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_279 1 FMT H 1 0.22 1.008
2 opls_271 1 FMT C 1 0.58 0.000
3 opls_272 1 FMT O1 1 -0.9 15.9994
4 opls_272 1 FMT O2 1 -0.9 15.9994
5 MW 1 FMT D 1 0.0 12.011
Should I use some constraints for "dummy mass" to define its position
in simulation? And can I get "dummy mass" type from ffoplaa.atp or
its better to add the new one?
Have you tried naming it an atom instead of a virtual site?
I`m sorry, I`ve read manual and corresponding article but I have not
find irrefragable answer for my questions.
Thanks
------------
Nilov Dmitri
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
-----------------------------------------------------
-----Original Message-----
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).
--
David van der Spoel, Ph.D.
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