lina wrote:
On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
lina wrote:
On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
lina wrote:
Hi,
Form the begining to 50000 steps, during EM, all exit in atom 8524,
how do I check it further? I mean, from which parts to examine?
I also switched to double version to run the EM.
Open your structure in a visualization program and look at what it might
be
clashing with
Thanks, I checked before.
And what did you find? What is the closest atom to the one with the maximal
force? Would its charge cause repulsion? Is it so close that LJ overlap is
causing a problem? In this case, visualization of the problematic structure
is the solution, you just have to take care to identify the source of the
problem. It certainly may not always be obvious.
Thanks, I guess I might make the system so compact.
Before in VMD it showed something weird, kind of broken bond, but in
PyMOL was fine.
Well, the bond didn't actually break, but that's clearly where the problem is.
You have some sort of geometric strain. The EM process should have produced a
.trr file, which, if you saved coordinates frequently enough, should let you see
how that strained structure evolved.
-Justin
Thanks again,
-Justin
-Justin
....
Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04,
atom=
8524
...
Step=42313, Dmax= 2.0e-10 nm, Epot= -2.17267e+05 Fmax= 2.23506e+04,
atom=
8524
...
Step=50000, Dmax= 1.7e-10 nm, Epot= -2.17267e+05 Fmax= 2.89751e+04,
atom=
8524
writing lowest energy coordinates.
Steepest Descents did not converge to Fmax < 1000 in 50001 steps.
Potential Energy = -2.17266924593509e+05
Maximum force = 2.89751132744731e+04 on atom 8524
Norm of force = 2.18622026854678e+02
Thanks for any advice,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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