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" <[email protected]>
Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
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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
========================================
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