[gmx-users] pdb2gmx and virtual sites

[Ondrej Marsalek]

On Wed, Nov 4, 2009 at 20:41, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Ondrej Marsalek wrote:
>>
>> I thought that this was needed to convert the hydrogens to virtual
>> sites, based on reading section 6.5 of the manual and some other
>> things. Is this not correct?
>>
>
> I don't believe constraining angles is necessary.  The manual only refers to
> fixed bond lengths.

Perhaps we are talking about different things, but looking at the 2nd
paragraph of section 6.5 (page 127):

"For the remaining degrees of freedom, the shortest oscillation period
as measured from a simu-
lation is 13 fs for bond-angle vibrations involving hydrogen atoms."

And then later on in section 6.5.1:

"The goal of defining hydrogen atoms as virtual sites is to remove all
high-frequency degrees of
freedom from them."

As far as I understand the procedure, the hydrogens can only be
converted to virtual sites if the angles are constrained, because only
then is their position uniquely given by the positions of heavy atoms.

> If you're looking for an example to follow, I would
> suggest running the lysozyme benchmark described in the GROMACS 4 paper; the
> parameters used are nicely detailed.

Thanks for the suggestion, will have a look at that.

Ondrej


> I got reasonable results using
> "constraints = all-bonds," but if that is not correct, perhaps someone else
> can comment.
>
> -Justin
>
>> Ondrej
>>
>>
>> On Wed, Nov 4, 2009 at 20:07, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> Ondrej Marsalek wrote:
>>>>
>>>> Dear GROMACS users,
>>>>
>>>> I would like to substitute hydrogens in a protein with virtual sites
>>>> to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and
>>>> several other places. So far, I have not found an example or a
>>>> tutorial that would involve this, so I want to create a
>>>> straightforward example. I have taken the 2KO3 structure from the PDB
>>>> and went through this sequence of commands:
>>>>
>>>> pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p
>>>> -vsite hydrogens -ignh
>>>> editconf -f initial-vacuum.gro -o initial-box.gro -c -d 1 -bt cubic
>>>> genbox -cp initial-box.gro -cs tip4p.gro -p topol.top -o conf.gro
>>>> grompp
>>>>
>>>> I also provided a pretty standard grompp.mdp, that contains
>>>> "constraints = h-angles". I get the following error:
>>>>
>>>> -------------------------------------------------------
>>>> Program grompp, VERSION 4.0.5
>>>> Source code file: vsite_parm.c, line: 779
>>>>
>>>> Fatal error:
>>>> Automatic parameter generation not supported for Virtual site 3 atom 4
>>>> for this bonding configuration
>>>> -------------------------------------------------------
>>>>
>>>> I am not sure what the problem is. I would appreciate and help on the
>>>> use of this feature, pointers to resources, or a working example.
>>>> Reading the manual and searching did not help as much as I would like.
>>>>
>>> Have you tried specifying either "all-bonds" or "h-bonds" for
>>> constraints?
>>>  I think "all-bonds" is the most commonly-used option.  Any specific
>>> reason
>>> for using "h-angles"?
>>>
>>> -Justin
>>>
>>>> Thanks,
>>>> Ondrej
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>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
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