Hi Ray,
Thanks for the report ...
Curious ... Unfortunately, I cannot run Amber12 anymore to rerun our
original calculations now but we do have significant differences between
Amber12 (calculated back in 2013-2014) and Amber14 (calculated now)
....I will try to reinstall amber12 to see if I can confirm the
differences ....
Best,
Vlad
On 10/18/2016 07:47 PM, Ray Luo wrote:
> Vlad,
>
> In my initial trial (using five snapshots, every 10000 frames) of all
> three releases, amber12, amber14, and amber16, only amber16 gives
> different EEL (i.e. EELEC + EPB). Indeed the differences between
> amber16 and the other two releases are larger than what we saw in the
> test cases. I'm turning on the verbal mode to see what is the cause.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Fri, Oct 14, 2016 at 11:29 AM, Ray Luo <rluo.uci.edu> wrote:
>> Vlad,
>>
>> Looks like your input parameters are reasonably set. If you see much
>> higher differences among different releases for your system, maybe you want
>> to email your inpcrd/prmtop files to me OFF THE LIST so I can see
>> what's the cause.
>>
>> All the best,
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor
>> Biochemistry, Molecular Biophysics, Chemical Physics,
>> Chemical and Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Fri, Oct 14, 2016 at 10:35 AM, Vlad Cojocaru
>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>> Hi Ray,
>>>
>>> Now I don't have access to the computers but the differences I am seeing
>>> in the deltaG are from -26 (amber12), to -40 (amber14), to -77 (amber16)
>>> .... As the only difference in the outputs are in the EEL energy (all
>>> other terms are identical), this is a change of 200% percent with each
>>> Amber version ...
>>>
>>> But I will take a look again at the test cases on Monday and try to
>>> rationalize further ...
>>>
>>> Its a little frustrating because I was quite happy with the values we
>>> got using Amber 12 and now it turns out that simply changing the version
>>> of the program we use, we get huge differences to our original results
>>> ... Maybe the ddGs or dddGs we reported in the Structure paper 2014 are
>>> unaffected (did not do a full test for that yet) but still it is
>>> frustrating to see such differences by just changing the version of the
>>> program .....
>>>
>>> Best
>>> Vlad
>>>
>>> On 10/14/2016 06:34 PM, Ray Luo wrote:
>>>> Hi Vlad,
>>>>
>>>> I found the reason of the discrepancy. If you look at the standard
>>>> nonlinear PB test cases (under AmberTools/test/pbsa_npb), they are
>>>> consistent between amber12 and amber14. While working on his NPB/P3M
>>>> algorithm for the amber16 release, my student, Li Xiao, found a flip
>>>> of sign in the bulk ion energy calculation. You can find his comment
>>>> in routine pb_ionene() within "pb_nlsolver.F90". After his fix, we see
>>>> a change about 0.7% in the total EELEC energies in our test cases.
>>>> I'll confirm with him again regarding this.
>>>>
>>>> All the best,
>>>> Ray
>>>> --
>>>> Ray Luo, Ph.D.
>>>> Professor
>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>> Chemical and Biomedical Engineering
>>>> University of California, Irvine, CA 92697-3900
>>>>
>>>>
>>>> On Fri, Oct 14, 2016 at 8:44 AM, Ray Luo <rluo.uci.edu> wrote:
>>>>> Vlad,
>>>>>
>>>>> As for the P3M approach, you probably don't want to freely adjust the
>>>>> cutoff distance because the nonbonded list is shared between direct
>>>>> pairwise sum and surface generation routines.
>>>>>
>>>>> I'm looking at your input files right now. In general, we have mostly
>>>>> focussed on the default setup that is used by most users to ensure
>>>>> consistency between releases. Other rarely used options are not tested
>>>>> often. Maybe we should put your test into the release test cases so we
>>>>> can check it every time the code is changed. What do you think?
>>>>>
>>>>> All the best,
>>>>> Ray
>>>>> --
>>>>> Ray Luo, Ph.D.
>>>>> Professor
>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>>> Chemical and Biomedical Engineering
>>>>> University of California, Irvine, CA 92697-3900
>>>>>
>>>>>
>>>>> On Fri, Oct 14, 2016 at 1:42 AM, Vlad Cojocaru
>>>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>>>> Thanks ...
>>>>>>
>>>>>> Sorry, I need to ask another question ... I am now playing with lots of
>>>>>> parameters and in one run I set cutnb to a higher value (with eneopt =
>>>>>> 4) but I get an error that points me to a "cutres" option which I could
>>>>>> not find in the manual.
>>>>>>
>>>>>> Could you please let me know me what the "cutres" option is ?
>>>>>>
>>>>>> Thanks
>>>>>> Vlad
>>>>>>
>>>>>> On 10/14/2016 12:23 AM, Ray Luo wrote:
>>>>>>> I'm teaching this quarter and haven't got a time to look at your
>>>>>>> files, but I'll look at your example next ...
>>>>>>>
>>>>>>> It's most likely due to the different default optimal values and/or
>>>>>>> bug fixes ... I will run your jobs without specifying any parameters
>>>>>>> first to see whether the default behaviors are similar. This is how
>>>>>>> new releases were first tested against previous versions. When you
>>>>>>> specify most not not all parameters explicitly, the default behaviors
>>>>>>> would get changed somewhat.
>>>>>>>
>>>>>>> As for speedup in Amber16, yes, this is due to a major code cleanup to
>>>>>>> organize the modules better.
>>>>>>>
>>>>>>> All the best,
>>>>>>> Ray
>>>>>>> --
>>>>>>> Ray Luo, Ph.D.
>>>>>>> Professor
>>>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>>>>> Chemical and Biomedical Engineering
>>>>>>> University of California, Irvine, CA 92697-3900
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Oct 13, 2016 at 8:43 AM, Vlad Cojocaru
>>>>>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>>>>>> Dear Ray, Dear all,
>>>>>>>>
>>>>>>>> I also performed exactly the same calculation I described in my original
>>>>>>>> mail with Amber 14 .. Every version of Amber provides different values for
>>>>>>>> the electrostatic energies although the run was done with exactly the same
>>>>>>>> scripts, on exactly same topologies and trajectory .. Moreover, almost all
>>>>>>>> pbsa parameters are specified explicitly in the input MDIN file (see again
>>>>>>>> original mail below) ...
>>>>>>>>
>>>>>>>> Best wishes
>>>>>>>> Vlad
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 10/13/2016 10:47 AM, Vlad Cojocaru wrote:
>>>>>>>>> Hi Ray,
>>>>>>>>>
>>>>>>>>> It would be great if we could understand where these differences come
>>>>>>>>> from ...I looked at all parameters from my customized MDIN file (which I
>>>>>>>>> attached to my original mail below) and I did not notice any change
>>>>>>>>> between Amber 12 and Amber 16 in terms of the meaning of the values
>>>>>>>>> (hope I did not miss anything). I am now doing the same calculation
>>>>>>>>> with Amber 14 as well to see if the difference came between Amber 12 and
>>>>>>>>> Amber 14 or between Amber 14 to Amber 16 ...
>>>>>>>>>
>>>>>>>>> On a side note, the calculation is much faster with Amber 16 comparing
>>>>>>>>> to Amber 14 ... Is that to be expected ?
>>>>>>>>>
>>>>>>>>> Thanks for looking into this
>>>>>>>>> Vlad
>>>>>>>>>
>>>>>>>>> On 10/12/2016 10:44 AM, Ray Luo wrote:
>>>>>>>>>> Hi Vlad,
>>>>>>>>>>
>>>>>>>>>> Thanks a lot for letting us know! I suppose the default was changed in
>>>>>>>>>> the script or the code. Will let you know the cause.
>>>>>>>>>>
>>>>>>>>>> All the best,
>>>>>>>>>> Ray
>>>>>>>>>> --
>>>>>>>>>> Ray Luo, Ph.D.
>>>>>>>>>> Professor
>>>>>>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>>>>>>>> Chemical and Biomedical Engineering
>>>>>>>>>> University of California, Irvine, CA 92697-3900
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Oct 12, 2016 at 1:31 AM, Vlad Cojocaru
>>>>>>>>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>>>>>>>>> Dear all,
>>>>>>>>>>>
>>>>>>>>>>> I am trying to reproduce some of our previous MMPBSA calculations with
>>>>>>>>>>> Amber
>>>>>>>>>>> 16. Original calculations were done in Amber 12. Now, using exactly the
>>>>>>>>>>> same
>>>>>>>>>>> trajectory, exactly same topology files, exactly the same input files
>>>>>>>>>>> (see
>>>>>>>>>>> below the MMPBSA input as well as the customized MDIN), I get an
>>>>>>>>>>> absolute
>>>>>>>>>>> affinity (without entropy) of -77 kcal/mol versus previously calculated
>>>>>>>>>>> -26
>>>>>>>>>>> kcal/mol ... The only difference between the runs in actually in the
>>>>>>>>>>> electrostatic energy (-43.5 in the new calculation versus +8 in the old
>>>>>>>>>>> calculation) . See attached output files.
>>>>>>>>>>>
>>>>>>>>>>> Therefore, the problem (or difference) is in the PB solver in Amber 16
>>>>>>>>>>> versus Amber 12 ... Does anybody have any idea where the difference
>>>>>>>>>>> could
>>>>>>>>>>> come from ??
>>>>>>>>>>>
>>>>>>>>>>> I know that one should not put too much weight on the absolute values,
>>>>>>>>>>> but
>>>>>>>>>>> still running with exactly the same scripts, exactly same topology
>>>>>>>>>>> files,
>>>>>>>>>>> exactly the same old trajectory in 2 different versions of the same
>>>>>>>>>>> program
>>>>>>>>>>> should give the same results ....
>>>>>>>>>>>
>>>>>>>>>>> Thanks for any insights in this
>>>>>>>>>>>
>>>>>>>>>>> Best wishes
>>>>>>>>>>> Vlad
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ---- MMPBSA INPUT -----
>>>>>>>>>>> MMPBSA
>>>>>>>>>>> &general
>>>>>>>>>>> debug_printlevel=1,
>>>>>>>>>>> startframe=${startframe},
>>>>>>>>>>> endframe=${endframe},
>>>>>>>>>>> interval=${interval},
>>>>>>>>>>> keep_files=1,
>>>>>>>>>>> netcdf=1,
>>>>>>>>>>> ligand_mask=":${r1_ligand}-${r2_ligand}",
>>>>>>>>>>> receptor_mask=":${r1_receptor}-${r2_receptor}",
>>>>>>>>>>> use_sander=1,
>>>>>>>>>>> entropy=0,
>>>>>>>>>>> full_traj=1,
>>>>>>>>>>> verbose=2,
>>>>>>>>>>> /
>>>>>>>>>>> &pb
>>>>>>>>>>> inp=2,
>>>>>>>>>>> cavity_offset=-0.5692,
>>>>>>>>>>> cavity_surften=0.0378,
>>>>>>>>>>> indi=4.0,
>>>>>>>>>>> exdi=80.0,
>>>>>>>>>>> fillratio=4.0,
>>>>>>>>>>> istrng=0.100,
>>>>>>>>>>> linit=1000,
>>>>>>>>>>> prbrad=1.4,
>>>>>>>>>>> radiopt=1,
>>>>>>>>>>> scale=2.0,
>>>>>>>>>>> /
>>>>>>>>>>>
>>>>>>>>>>> $MPI_HOME/bin/mpirun -n $NSLOTS $AMBERHOME/bin/MMPBSA.py.MPI -O -i
>>>>>>>>>>> mmpbsa_${run}.in \
>>>>>>>>>>> -o
>>>>>>>>>>> mmpbsa_${run}.out \
>>>>>>>>>>> -cp
>>>>>>>>>>> ${top_complex} \
>>>>>>>>>>> -rp
>>>>>>>>>>> ${top_receptor} \
>>>>>>>>>>> -lp
>>>>>>>>>>> ${top_ligand} \
>>>>>>>>>>> -y
>>>>>>>>>>> ${traj_complex} \
>>>>>>>>>>> -eo
>>>>>>>>>>> energy_${run}.out \
>>>>>>>>>>> -use-mdins
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ---- MDIN ------------------------
>>>>>>>>>>> MMPBSA, Nonlinear PB, inp=2, sasopt=2
>>>>>>>>>>> &cntrl
>>>>>>>>>>> nsnb=99999, dec_verbose=0, ioutfm=1,
>>>>>>>>>>> ipb=2, ntb=0, cut=999.0, imin=5,
>>>>>>>>>>> igb=10, inp=2,
>>>>>>>>>>> /
>>>>>>>>>>> &pb
>>>>>>>>>>> epsin=4, epsout=80, smoothopt=1,
>>>>>>>>>>> istrng=100.0, pbtemp=300, radiopt=1,
>>>>>>>>>>> dprob=1.4, iprob=2.0, sasopt=2, saopt=0,
>>>>>>>>>>> triopt=1, arcres=0.25,
>>>>>>>>>>> npbopt=1, solvopt=1, accept=0.001,
>>>>>>>>>>> maxitn=100, fillratio=4.0, space=0.5,
>>>>>>>>>>> nbuffer=0, nfocus=2, fscale=8, npbgrid=1,
>>>>>>>>>>> bcopt=5, eneopt=1, frcopt=0, scalec=0,
>>>>>>>>>>> cutfd=5.0, cutnb=12, nsnba=1,
>>>>>>>>>>> phiout=0,
>>>>>>>>>>> decompopt=2, use_rmin=1, sprob=0.557, vprob=1.3,
>>>>>>>>>>> rhow_effect=1.129, use_sav=1,
>>>>>>>>>>> cavity_surften=0.0378, cavity_offset=-0.5692,
>>>>>>>>>>> maxsph=400,
>>>>>>>>>>> /
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Dr. Vlad Cojocaru
>>>>>>>>>>> Computational Structural Biology Laboratory
>>>>>>>>>>> Department of Cell and Developmental Biology
>>>>>>>>>>> Max Planck Institute for Molecular Biomedicine
>>>>>>>>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>>>>>>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>>>>>>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>>>>>>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>> --
>>>>>>>> Dr. Vlad Cojocaru
>>>>>>>> Computational Structural Biology Laboratory
>>>>>>>> Department of Cell and Developmental Biology
>>>>>>>> Max Planck Institute for Molecular Biomedicine
>>>>>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>>>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>>>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>>>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>> --
>>>>>> Dr. Vlad Cojocaru
>>>>>> Computational Structural Biology Laboratory
>>>>>> Department of Cell and Developmental Biology
>>>>>> Max Planck Institute for Molecular Biomedicine
>>>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> --
>>> Dr. Vlad Cojocaru
>>> Computational Structural Biology Laboratory
>>> Department of Cell and Developmental Biology
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Oct 18 2016 - 14:30:02 PDT
