[gmx-users] Virtual site and constraints
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jan 23 21:30:29 CET 2008
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.
> 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:
>>>>> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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