Fabio Affinito wrote:
On 07/26/2011 07:02 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
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.
Yes, but this doesn't make things easier! :-)
According to the log the atoms to consider are 159986 and 159990
That's not what you posted before. The .log output indicated atoms
193657 and 193660 were problematic.
Sorry. It's because I've tried with many systems (with different -nbox
values) and the error was always the same.
Browsing the conf.gro, if I didn't make mistakes this atoms are:
30040POPG OE59986 0.080 13.158 2.964 0.0885 0.4154 -0.0859
30040POPG C1C59990 0.219 26.034 3.221 0.6449 0.0750 0.1313
But their distance is 12.8nm, while md.log reports 38.911 nm...
In any case, why are atoms four bonds (based on the original .log output
of 1-4 interactions being a problem) away separated by 12.8 nm? Seems
very odd to me. I ask yet again - what are your box vectors, before and
after manipulation with genconf?
Seems odd to me, too. For the box vectors (sorry if I didnt answer
before), in this case:
after: 26.04658 26.04658 8.75317
before: 13.02329 13.02329 8.75317
Hope it helps.
Without seeing the coordinate files, I can't tell anything further. If you
want, you can send me (off-list) the coordinate files before and after genconf
and please tell me the exact atoms that are reported as problematic.
-Justin
Best regards,
Fabio
-Justin
So what?
F.
-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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