[gmx-users] Assigning Improper Dihedrals to an Index Group

[Justin A. Lemkul]

Darrell Koskinen wrote:
> Hi Justin,
> I want to assign the improper dihedral "improper_Z_CA_X_Y" to all 
> dihedrals within an index group. I would prefer not to write code to 
> insert "1" into the "function type" field followed by the improper 
> dihedral reference. Is there a command I can issue that will insert the 
> correct function type code and improper dihedral reference into my .top 
> file for the dihedrals associated with a specific index group?
> 

Not that I know of; this hypothetical program would have to know all the bonded 
parameters to know which groups of four atoms are involved in those impropers. 
I don't know of any program other than pdb2gmx that can do anything remotely close.

It would, however, be a fairly trivial exercise with awk or perl to script this 
process.

-Justin

> Thanks in advance.
> 
> Darrell
>> Date: Mon, 27 Jul 2009 17:48:02 -0400
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4A6E2092.402 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> Darrell Koskinen wrote:
>>  
>>> Hi Justin,
>>> With regard to your comment about using other force fields for my 
>>> simulation of graphene surrounded by ammonia gas, are referring to 
>>> the force fields for both graphene and ammonia or only to the force 
>>> field for graphene?
>>>
>>>     
>>
>> The "force field" should be one in the same.  The parameters should be 
>> suitably derived using the same scheme as the original work.
>>
>>  
>>> I reviewed my selection of the force field parameters for graphene 
>>> and see that I selected the parameters from the paper by Cornell et 
>>> al. since a paper on deformation of carbon nanotubes ("A structural 
>>> mechanics approach for the analysis of carbon nanotubes" by Chunyu 
>>> Li, Tsu-Wei Chou in International Journal of Solids and Structures 40 
>>> (2003) 2487–2499) used parameters from the paper by Cornell et al. Is 
>>> this sufficient to justify the use of these parameters? I also 
>>> thought that graphene and ammonia would be considered organic since 
>>> they are comprised of carbon, nitrogen, and hydrogen, which are all 
>>> common elements found in organic matter.
>>>
>>>     
>>
>> If you feel that precedent is sufficient, then I guess go ahead.  But 
>> realize that the paper by Cornell et al. refers to parameters suitable 
>> for simulations of proteins and nucleic acids, as well as a few 
>> organic functional groups. Parameterization was based on peptide 
>> backbone geometry, as well as other parameters, likely none of which 
>> involved graphene and gaseous ammonia (they were doing liquid 
>> simulations).
>>
>>  
>>> With regard to the parameters for ammonia, is it acceptable to use 
>>> the parameters from the paper by Cornell et al. or do I need to find 
>>> papers specifically related to ammonia gas molecular dynamics 
>>> simulations?
>>>
>>>     
>>
>> I would seriously consider finding parameters (if they exist) that 
>> have been derived for use with gas-phase simulations.
>>
>>  
>>> With regard to dihedral selection, I looked at the .top file and see 
>>> that the function type is listed as 3 in the dihedrals section, which 
>>> I believe indicates that my simulation is using a Ryckaert-Bellemans 
>>> function. It appears to me that if I am using the OPLS force field 
>>> that the Ryckaert-Bellemans dihedral type is automatically selected. 
>>> I do see in the ffoplsaabon.itp file that there is an improper 
>>> dihedral definition which think I could potentially use in my 
>>> simulation "improper_Z_CA_X_Y", but how do I cause my simulation to 
>>> use this definition? Do I need to add the following line to my .top 
>>> file?
>>> "#define improper_Z_CA_X_Y"
>>>
>>>     
>>
>> No, you would have to use a special dihedrals section, that specifies 
>> the four atoms involved (function type 1), followed by the 
>> specification of that particular improper ("improper_Z_CA_X_Y").  See 
>> the manual for more details, and/or generate a topology for a protein 
>> with pdb2gmx with OPLS-AA and see how they're defined.
>>
>>  
>>> Further, I thought that I could simply modify the appropriate lines 
>>> of the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters 
>>> found in the paper by Cornell et al. so that they will be used in my 
>>> simulation. Am I correct in my assumption?
>>>
>>>     
>>
>> Modifying ffoplsaa files to parameters that are not OPLS-AA is 
>> probably a bad choice.  If you're dead-set on using these parameters, 
>> download the ffamber ports and use the ffamber94 force field, not some 
>> Frankensteined-OPLS.  Besides, all of the parameters in the Cornell 
>> paper are in kcal/mol/A^2, which will require conversion to Gromacs 
>> standard units.  If you've printed them directly in your previous 
>> attempts, I can guarantee you you're not getting the values you think 
>> you are.
>>
>> -Justin
>>
>>  
>>> Thanks again for your help.
>>>
>>> Darrell
>>>     
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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

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