[gmx-users] pdb2gmx and virtual sites

[Justin A. Lemkul]

Ondrej Marsalek wrote:
> 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."
> 

The quotes above define the problem, but I see no reference to using h-angles as 
your constraints.

> 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.
> 

See the following:

http://lists.gromacs.org/pipermail/gmx-users/2008-October/037569.html

-Justin

>> 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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> 

-- 
========================================

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

========================================