[gmx-users] Assigning Improper Dihedrals to an Index Group
darrellk at ece.ubc.ca
Sat Aug 8 04:07:39 CEST 2009
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.
>> Thanks again for your help.
More information about the gromacs.org_gmx-users