Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW99999 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638
Could this be the origin of my problem?
Atom numbering is not the problem. This happens all the time for systems of
hundreds of thousands of atoms, which Gromacs handles just fine. Please
investigate the points I suggested before.
-Justin
Thanks again,
Fabio
On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:
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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