Yanmei Song wrote:
What makes me so confused is that I used this top for the MD run using
ffoplsaa.itp and the there are no error message. Also I got a good
result compared to experiment. Does it mean that what I did is totally
wrong with using this top in combination with OPLS?
Well, the numbers in the .top for the dihedrals were designed to be components
of a periodic dihedral (function type 1 in the .top), which is not of the same
form as an R-B dihedral (function type 3). My guess would be that the
parameters you have specified are not appropriate for use with OPLS.
Also if I used the atom type in opls_x with the x is less than 135,
then it should be OPLS UA force field right? if I want to use OPLS,
How can we get the top? Thank you so much for your help!
I suppose you would have OPLS UA, as far as your atom types are concerned. I
don't know for sure, I've never used the UA version of OPLS. If you want the
.top for your own molecule, you may have to write it by hand, perhaps even using
the PRODRG topology as a skeleton (along with a thorough understanding of
Chapter 5 of the manual, as Mark advised). Depending on the size of your
molecule, this manual process may be a chore, so you could also consider making
an entry for your molecule within ffoplsaa.rtp. Make a local copy in the
working directory to ensure that you don't break something by accident!
-Justin
2009/1/28 Justin A. Lemkul <jalem...@vt.edu>:
Yanmei Song wrote:
Hi,Justin:
Thanks for your response.
I have read that part and still confused. Does it mean that if I
choose the ffoplsaa.itp in my top, I used the RB potential for
Dihedrals or the periodic type? Also actually I can only get the
parameters for phi, cp and mult (listed above) Can I use these
parameters directly for my itp user ffoplsaa force field? Thanks a
lot!
OPLS does use the R-B potential. It looks like that topology is a PRODRG
product, in which case, no, your topology is not suitable for use with OPLS.
PRODRG generates Gromos-type topologies.
-Justin
2009/1/28 Justin A. Lemkul <jalem...@vt.edu>:
Yanmei Song wrote:
Hi,
I am using ffoplsaa.itp as my force field to do a simulation using
GROMACS.
I have a question about how to write the parameters in dihedrals in
the itp file.
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 2 5 6 1 0.0 3.77 3 0.0 3.77 3 ; dih CAA
CBF OAW CBH
2 5 6 9 1 0.0 3.77 3 0.0 3.77 3 ; dih CBF
OAW CBH OAY
5 6 9 10 1 0.0 3.77 3 0.0 3.77 3 ; dih OAW
CBH OAY CBJ
6 9 10 13 1 0.0 3.77 3 0.0 3.77 3 ; dih CBH
OAY CBJ OBA
9 10 13 14 1 0.0 3.77 3 0.0 3.77 3 ; dih OAY
CBJ OBA CBL
Then if I am choosing ffoplsaa.itp force field, what is the meaning
for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and
OPLS force field have a different format for proper dihedrals. For
OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my
question is how can i define the dihedral parameters in itp file based
on ffoplsaa force field in GROMACS? Thanks a lot!
Refer to the manual, section 4.2.12 "Proper Dihedrals."
-Justin
Yanmei
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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
Graduate Research Assistant
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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or send it to gmx-users-requ...@gromacs.org.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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