hhhh huan wrote:
Dear all gmx users, developers, and Justin,
I have tried the OPLS_136 and this is the force field that caused the 2
warnings during grompp and I had also try the other parameters. I think that
should be needed a unique parameter development for this molecule.
So, I am still "headache" about this.
Any guide n comments will be appreciated.
Thank you
Well, you've already decided that you need to develop some new
parameters, so there's really nothing left to be said. Read the
paper(s) that deal with OPLS force field development, and follow what
was done with respect to the parameter(s) you need to develop.
Be warned, this is an advanced topic, and I doubt your "headache" will
go away any time soon :-)
-Justin
--- On Sat, 7/5/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: segmentation fault during MD and develop parameter
To: [EMAIL PROTECTED]
Date: Saturday, July 5, 2008, 6:38 PM
It seems like there should be something special about that
location - a
tetrahedral center flanked by two rigid groups, but I
don't know just
how important that necessarily is. Have you tried just
assigning the
normal parameters for an alkane CH2 group (opls_136) to
your atom in
question?
Just an idea, but I have no idea if this is a unique
situation that
requires unique parameter development.
-Justin
hhhh huan wrote:
Dear all Gmx users n developers,
I am happy and appreciate with all the help n
suggestions you all have given to me.
Here is my molecule look likes.:
C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C
|
O
|
C-C-C-C-C-C=C-(c)-C=C-C-C-C-C-C-C-C-C=O
The problem that i faced now is the parameter of the
OPLS-AA force field for the carbon atom which is in the
bracket . I am now still looking for the solutions for this
problem.
Any guide n comments will be appreciated.
Thanks
--- On Fri, 7/4/08, Justin A. Lemkul
<[EMAIL PROTECTED]> wrote:
From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: [gmx-users] Re: segmentation fault during
MD and develop parameter
To: "Gromacs Users' List"
<[email protected]>
Date: Friday, July 4, 2008, 10:13 PM
hhhh huan wrote:
Dear all Gmx users n developers,
I am a beginner of Gromacs user, hence I am
quite new
to the system..May i know how to develop the
missing
dihedral parameter?
Any guide n comments will be appreciated.
Thanks
No one here is going to be able to help, aside
from the
standard, "Yes,
you can do it if you read the original paper for
the force
field you
want to use." If you describe your molecule
and what
the missing
parameter is (functional group, etc.), then maybe
someone
will have an
insight.
Otherwise, you're in for some
parameterization, which
is not recommended
for the novice user.
-Justin
--- On Fri, 7/4/08, Justin A. Lemkul
<[EMAIL PROTECTED]> wrote:
From: Justin A. Lemkul
<[EMAIL PROTECTED]>
Subject: Re: [gmx-users] segmentation
fault during
MD
To: [EMAIL PROTECTED],
"Discussion list
for GROMACS users"
<[email protected]>
Date: Friday, July 4, 2008, 6:41 PM
hhhh huan wrote:
Dear gmx users and developers.
I was running a simulation with 5 ns.
But it
stated
"segmentation fault" at time
around 1
ns, and the
simulation was stopped.
By the way, i faced 2 warning during
running
the
Grompp, it stated there:" warning 1
No
default
Ryckaert-Bell types, using zeroes"
File 'p1.top' , line
209
warning 2 No default Ryckaert-Bell
types,
using
zeroes"
File 'p1.top' , line
210
i know that thses are the missing
force field
parameter at the indicated line,but i keep
on
running the
simulation and the segmentation fault
appeared
because i
cant find any force field that is suitable
for the
particular atoms. However, I manage to
finish the
energy
minimization.
So, is it the segmentation fault has
anything
to do
with the 2 warning? or there is any other
way to
solve my
problems?
You need to find/develop parameters for
the
missing
dihedral
parameters. Running a simulation with
missing
information
will likely
lead to inaccurate/questionable results.
As for whether that directly lead to the
segmentation
fault, that's
difficult to diagnose, but I would start
by
getting the
missing
parameters to eliminate it as a
possibility.
-Justin
Thanks a lot
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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
========================================
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search
before posting!
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the list.
Use the
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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
========================================
--
========================================
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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Please search the archive at http://www.gromacs.org/search before posting!
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