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

Darrell Koskinen darrellk at ece.ubc.ca
Sat Aug 8 04:07:39 CEST 2009

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?

Thanks in advance.

> 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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