Fabio Affinito wrote:
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)
By whole, I mean that the molecules are not split across periodic
boundaries in the initial configuration that you replicated. If you
replicate a periodic break, then you split the molecules by a distance
equal to the new periodic distance.
-Justin
Ok, so: no, it's not broken.
What you need to do is use the information mdrun provided you to diagnose what's
going on. Apparently atoms 193657 193660 are separated by 31 nm. What are your
box vectors? Where are these atoms in the system? Then you'll have your
answer. The only reason I can think of for such extreme distances is a
periodicity issue.
-Justin
--
========================================
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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