Please make sure to keep the discussion on the list.
Fabio Affinito wrote:
Justin,
first of all, I thank you very much for your help: it's very precious. I
regret I didn't notice before the molecule was broken.
I suggested to you yesterday that your initial configuration was broken. You
told me it wasn't.
Unfortunately the problem is not solved with your recipe. I used trjconv
on the starting configuration and then I used the genconf.
The mdrun fails with the same error. In this case, the atoms involved in
the error are not the same of the previous one. But once again the bond
length is completely odd.
During the grompp I had some warning, but I can't understand where they
are coming from:
Certain bonded interactions can't take place between massless particles. As the
warning states, if pdb2gmx produced the topology, don't worry about it.
Cleaning up constraints and constant bonded interactions with virtual
sites
Removed 1305 Angles with virtual sites, 6251 left
Removed 480 Proper Dih.s with virtual sites, 363 left
Converted 2230 Constraints with virtual sites to connections,
2596 left
Warning: removed 582 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this
warning
Cleaning up constraints and constant bonded interactions with virtual
sites
Removed 1305 Angles with virtual sites, 6251 left
Removed 480 Proper Dih.s with virtual sites, 363 left
Converted 2230 Constraints with virtual sites to connections,
2596 left
Warning: removed 582 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this
warning
Cleaning up constraints and constant bonded interactions with virtual
sites
Removed 1305 Angles with virtual sites, 6251 left
Removed 480 Proper Dih.s with virtual sites, 363 left
Converted 2230 Constraints with virtual sites to connections,
2596 left
Warning: removed 582 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this
warning
Cleaning up constraints and constant bonded interactions with virtual
sites
Removed 1305 Angles with virtual sites, 6251 left
Removed 480 Proper Dih.s with virtual sites, 363 left
Converted 2230 Constraints with virtual sites to connections,
2596 left
Warning: removed 582 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this
warning
According to your experience, this can be pertinent with my problems?
Not likely. The virtual sites are within the protein, not the lipids, right?
Without the mdrun output, there's little else I can tell you.
-Justin
Thank you once again,
Fabio
On 07/27/2011 02:45 PM, Justin A. Lemkul wrote:
The problem is indeed as I suspected. Your molecules are broken across
periodic boundaries in the initial configuration. When you replicate
with genbox, you've now replicated broken molecules such that those at
the new interfaces between the boxes appear to be intact, but in fact
they are not. This is just an artifact of visualization. If you use
"trjconv -pbc whole" on the original starting configuration to make the
molecules whole before replicating with genconf -nbox, you will avoid
this problem.
-Justin
Fabio Affinito wrote:
Yes. It's in attachment.
Fabio
On 07/27/2011 02:38 PM, Justin A. Lemkul wrote:
Can you please also send me the coordinate file from before you ran
genconf?
-Justin
Fabio Affinito wrote:
Finally, I just got the right compression to fit my file in an
attachment.
The interesting lines are:
159988 and 159992
Kindly regards,
Fabio
On 07/27/2011 01:42 PM, Justin A. Lemkul wrote:
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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