On Tue, Apr 10, 2018 at 2:50 PM, Alexander Alexander
<alexanderwie...@gmail.com> wrote:
>
> Hi Christoph,
>
> On Tuesday, April 10, 2018 at 4:28:30 PM UTC-4, Christoph Junghans wrote:
>>
>> On Sun, Apr 8, 2018 at 8:17 PM, Alexander Alexander
>> <alexand...@gmail.com> wrote:
>> >
>> > Thanks Christoph.
>> >
>> > I know they are zero, and
>> >
>> >> <alexand...@gmail.com> wrote:
>> >> >
>> >> > Dear all,
>> >> >
>> >> > The potential_shift.pl crashes in IBI for some of the bond and angles
>> >> > in
>> >> > step 5, I have already seen a suggestion in mailing list such that
>> >> > "one
>> >> > should pick the minimum of the interaction (min property) bigger than
>> >> > 0,
>> >> > so
>> >> > that the target rdf is bigger than 0 as well" (although the crash for
>> >> > this
>> >> > old discussion happened in the step_001). If with minimum of the
>> >> > interaction
>> >> > you mean is the <min>XXXX</min> in the settings.xml file, then it is
>> >> > already
>> >> > more that 0 in may case (<min>2.713</min>). Also in general I did not
>> >> > understand the solutions proposed over there. So, I have attached
>> >> > here
>> >> > some
>> >> > steps of evolution of the problematic angel during IBI, and I would
>> >> > be
>> >> > so
>> >> > appreciated if one could help overcome the problem.
>> >> Looking at your inverse.log: above the error banner "No valid value
>> >> found in angle-H-L-RG.dpot.pure_ibi"
>> >> Looking at angle-H-L-RG.dpot.pure_ibi, all values are marked "o".
>> >> angle-H-L-RG.dist.tgt looks ok, but step_005/angle-H-L-RG.dist.new is
>> >> all
>> >> zeros.
>> >> So why that is I don't know, but you might want to run csg_stat by
>> >> hand:
>> >
>> > Yes, they are all zero.
>> >
>> >>
>> >> csg_stat --nt 32 --options
>> >> /home/alex/test/CG/dw/jeffamine-n2/ATB/ibi1/settings.xml --top
>> >> topol.tpr --trj tra
>> >> j.xtc --begin 50 --first-frame 0 --cg
>> >> /home/alex/test/CG/dw/jeffamine-n2/ATB/ibi1/jeffamine2-cg.xml
>> >
>> > Invoking this show nothing again all zero, while invoking this in
>> > step_004
>> > results to a nonzero output. From step 004 to 005 the only thing which
>> > change is the traj.xtc, so it might be something with the mdrun over the
>> > system.
>> My guess is that your system is slowly exploding in step 5 and hence
>> there are no value for the angle in range you specified in the xml
>> file.
>
> Thanks for getting back to me, I am getting such an error over an over now
> and no success yet just wasting my time.
> Indeed, even if do not get the potential_shift error, the system crashes at
> some points later in step_008 or so, with an error like "There is no domain
> decomposition for" or "bond missing" which are the sign of explosion, even
> minimization also do not help. But I am sure that the conf.gro comes from a
> very well equlibrated system (around 9 ns of NVT and NPT equilibrations show
> a converge density for the system agreeing with experiment), and most
> importantly, the MD simulation in each step of CG is in NVT ensemble, so, I
> do not know why explosion should happen in an NVT ensemble.
>
> Would you please let me know the order of potential for a bond like
> "bond-RB-RA" in each step?
> I mean for this bond a bond-RB-RA.pot.new will be generated in the step_000,
> then this bond-A-B.pot.new ---cp--> bond-RB-RA.pot.cur (in step_001) .... .
> Or in other word, what is the order of the below potential for this bond,
> which is result of which?
> bond-RB-RA.dist.new                     bond-RB-RA.dist.tgt_smooth.ijT3P
> bond-RB-RA.pot.extrapol.Rh1pt           bond-RB-RA.pot.smooth.sXbTa
> bond-RB-RA.dist.tgt                     bond-RB-RA.dpot.pure_ibi
> bond-RB-RA.pot.interpol.0S35s
> bond-RB-RA.dist.tgt_extrapolated.Q1VJa  bond-RB-RA.pot.cur
> bond-RB-RA.pot.shift.V6IRk
Just look into inverse.log:
$ grep bond-RB-RA inverse.log

>
> Also, which version of gromacs you are using? mine is 2018.1
I don't think, this has anything to do with your gromacs version.
Try to do IBI on non-bonded interaction only using bonded interactions
from simple BI.

Christoph
>
> Best regards,
> Alex
>>
>>
>> Christoph
>> >
>> >>
>> >> (from inverse.log)
>> >> my guess is that something in wrong in jeffamine2-cg.xml, which should
>> >> be a 1:1 mapping on the cg level.
>> >
>> > If that is the case why this does not happen in the steps before? As
>> > they
>> > are using the same jeffamine2-cg.xml.
>> > Anyway, I have attached both jeffamine2-cg.xml jeffamine2-aa.xml.
>> >
>> > Best regards,
>> > Alex
>> >>
>> >> Christoph
>> >> > Thank you.
>> >> > Regards,
>> >> > Alex
>> >> >
>> >> > --
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>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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-- 
Christoph Junghans
Web: http://www.compphys.de

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