Cun Zhang wrote:
hi, Justin. Thank you for your meticulous and patient explanation !
Before I see this post, I misunderstood the meaning of sharing bonds.
I thought note only the bonds,but also the angles and the dihedrals
should be added to top file.
I see now that I should have been more careful in my explanation. It is better
stated that *bonded parameters* should extend across periodic boundaries, not
just bonds. But the same principle applies.
It was so complicated to deal manually that I wrote that script.
That's sensible, but I didn't understand what your scripting was doing with
renumbering and all that. Just add the appropriate parameters to the .top,
given the numbering in the coordinate file.
I will read the doucment you mentioned carefully .
The CNT how-to was painstakingly assembled by Chris Stiles a few years ago after
many conversations like this one. He has done a nice service by assembling the
tutorial. I believe it applies to version 3.3.3, but many of the principles are
the same. Remember, as I suggested before, that x2top from the 3.3.3
distribution works with the -pbc option, which does all of the complicated work
for you. Not a bad option for your initial topology generation.
And I will fix these notes and warnings as grompp and mdrun suggest.
Good idea :)
-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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