[email protected] wrote:
Hi Justin,
"There is something physically unrealistic about your model"
You are right!
The main problem I found out is that some of the structures in my
Solution broke down......
I used ...
genbox -cp XXXX.grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top
-XXXXXX.gro
To generate multiple structures in a box. However, it creates overlap
and my orginal structures broke down. I checked the structures!
Using -ci and -cs simultaneously typically breaks down. Use -ci to add your
molecules, then in a separate step, use -cs to solvate the box.
-Justin
Can you please let me how to generate multiple structures in a fixed box
at random or packed in a solutio (e.g water)
Thank you for you help
Robella
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Hi Justin,
I tried to run full MD after energy minimization in both vacuo and
water... went good but I got this ERROR once I try to run full MD.
Can you please help.....
There is something physically unrealistic about your model. That's
the case whenever you see a LINCS warning. Without a more complete
description of what you've done (minimization and equilibration
protocol, initial construction of the model, etc) and the details of
your simulation parameters, there's nothing more anyone can really say
beyond a guess.
It appears that the wiki is down at the moment, but these pages have
useful information (when the site comes back up):
http://oldwiki.gromacs.org/index.php/blowing_up
http://oldwiki.gromacs.org/index.php/Errors
And since LINCS errors have been posted thousands of times to the
list, the archive should have some useful advice as well, so search here:
http://oldwww.gromacs.org/swish-e/search/search2.php
-Justin
--
========================================
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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--
========================================
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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