[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)
Mark Abraham
mark.j.abraham at gmail.com
Wed Mar 5 13:05:19 CET 2014
Thanks, Joao! (And David and Teemu!)
Mark
On Mar 5, 2014 11:11 AM, "João M. Damas" <jmdamas at itqb.unl.pt> wrote:
> Sorry, I shouldn't have embedded the plot. Here goes a link to it:
>
>
> https://dl.dropboxusercontent.com/u/3111184/plot_fixed_vs_nonfixed_g_sas.png
>
>
> On Wed, Mar 5, 2014 at 2:27 AM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
>
> > Thanks to Teemu, we found that the "-pbc yes" results is not a bug after
> > all (my bad). It is solved here: http://redmine.gromacs.org/issues/1449.
> > The final results are in Attached Table 4.
> >
> > To conclude, going back to the "-nopbc" bug found, the following plot is
> a
> > "real case" example of the difference one can see between a fixed and a
> > non-fixed g_sas run. I plot the contact area [there are several ways to
> > calculate this, I show one of them] between a ligand and a protein along
> > simulation time. Negative contact areas and the spikes were the puzzling
> > results I mentioned in the beginning of this thread.
> >
> > [image: Inline image 1]
> >
> > I would like to thanks David and Teemu for their help on this matter.
> >
> > Best,
> > João
> >
> > --
> > Attached Table 4
> > met - method used, anl=analytical method, num=numerical method (DCLM)
> > dots - number of points used for the numerical method
> > src - source of the data, paper=Eisenhaber1995, ASC=ASC software,
> > g463{sp,fx}=g_sas of GMX4.6.3 {single precision,fix 3199<
> https://gerrit.gromacs.org/#/c/3199/>
> > }
> >
> > pbc - PBC flag for g_sas, yes=-pbc, no=-nopbc
> > Areas are in square angstrom
> > ======================================================
> > met dots src pbc 4PTI 3FXN 1TIM
> > ======================================================
> > anl paper 3973.80 6943.80 20002.80
> > anl ASC 3973.81 6943.80 20002.80
> >
> > num 122 paper 3961.40 6968.30 19970.90
> > num 122 ASC 3961.44 6968.33 19970.90
> > num 122 g463sp yes 3957.81 6955.99 20004.20
> >
> > num 122 g463sp no 4169.21 7731.63 24080.20
> > num 122 g463fx yes 3957.81 6955.99 20004.20
> >
> > num 122 g463fx no 3957.81 6955.99 20004.20
> >
> > num 362 paper 3971.80 6933.40 19997.10
> > num 362 ASC 3971.79 6933.37 19997.10
> > num 362 g463sp yes 3969.92 6936.20 20016.70
> >
> > num 362 g463sp no 4195.02 7704.70 24132.10
> > num 362 g463fx yes 3969.92 6936.20 20016.70
> >
> > num 362 g463fx no 3969.92 6936.20 20016.70
> >
> > num 642 paper 3967.90 6944.40 19998.70
> > num 642 ASC 3967.78 6944.37 19998.70
> > num 642 g463sp yes 3966.21 6941.26 20013.40
> > num 642 g463sp no 4188.63 7701.99 24119.00
> > num 642 g463fx yes 3966.21 6941.26 20013.40
> > num 642 g463fx no 3966.21 6941.26 20013.40
> >
> >
> > num 1002 paper 3974.10 6939.10 20012.20
> > num 1002 ASC 3974.07 6939.12 20012.20
> > num 1002 g463sp yes 3973.51 6939.81 20027.50
> > num 1002 g463sp no 4193.60 7700.78 24143.10
> > num 1002 g463fx yes 3973.51 6939.81 20027.50
> > num 1002 g463fx no 3973.51 6939.81 20027.50
> >
> >
> > num 1472 paper 3975.70 6943.30 19997.00
> > num 1472 ASC 3975.70 6943.35 19996.90
> > num 1472 g463sp yes 3975.88 6943.96 20012.40
> >
> > num 1472 g463sp no 4198.08 7709.30 24123.30
> > num 1472 g463fx yes 3975.88 6943.96 20012.40
> >
> > num 1472 g463fx no 3975.88 6943.96 20012.40
> > ======================================================
> >
> >
> > On Tue, Mar 4, 2014 at 4:05 PM, João M. Damas <jmdamas at itqb.unl.pt>
> wrote:
> >
> >> Done: http://redmine.gromacs.org/issues/1449
> >>
> >> João
> >>
> >>
> >> On Tue, Mar 4, 2014 at 6:56 AM, David van der Spoel <
> spoel at xray.bmc.uu.se
> >> > wrote:
> >>
> >>> On 2014-03-04 04:39, João M. Damas wrote:
> >>>
> >>>> Hello Teemu,
> >>>>
> >>>> Thank you! I am glad the GROMACS team is concerned about this
> particular
> >>>> problem.
> >>>> And I am sorry for my late reply.
> >>>>
> >>>> For the sake of conciseness, so we do not get lost in the data, I am
> >>>> only
> >>>> showing the single precision results (we may bring double precision
> >>>> later
> >>>> on again). Also, since GROMACS 4.0.4 is flawed in the -pbc flag, as
> >>>> Teemu
> >>>> said, I also excluded it from these results (it is not going to get
> >>>> corrected anyway).
> >>>>
> >>>> I compiled a GROMACS version 4.6.3 with the fix presented in
> >>>> https://gerrit.gromacs.org/#/c/3199/ (in single precision).
> >>>>
> >>>> I repeated the tests and the results are presented in Attached Table
> 3.
> >>>>
> >>>> - the fix brings the -nopbc results close (within 1 square
> >>>> angstrom) to
> >>>>
> >>>> the ones obtained by ASC, except for 1TIM where the difference is
> >>>> within
> >>>> 10-20 square angstrom. Maybe 1TIM has a difficult shape, because
> >>>> ASC also
> >>>> had the largest difference between numerical DCLM and the
> >>>> analytical method
> >>>> in this protein.
> >>>> - the "-pbc yes" results though, do not change (which is normal,
> >>>>
> >>>> considering the flag is working in this version and the fix is
> >>>> inside a
> >>>> conditional expression that depends on the -pbc flag). It
> continues
> >>>> to
> >>>> baffle me why this is happening. If the molecule is inside the box
> >>>> and far
> >>>> from the edges (again, a test using a .gro created by editconf -d
> 5
> >>>> gave
> >>>> the same exact table as Attached Table 3), I see no reason why
> these
> >>>> results should be different...
> >>>>
> >>>> So, I think Bug #1445 <http://redmine.gromacs.org/issues/1445> is
> >>>> indeed
> >>>>
> >>>> solved, but we still need to solve an unknown bug with "-pbc yes".
> >>>> Should I
> >>>> open a new bug related to this in the redmine?
> >>>>
> >>>
> >>> In short, yes. If the protein is in the center of the box with no
> >>> periodic contacts the result should be the same as without pbc.
> >>>
> >>>
> >>>> I can perform more tests, if anyone has more ideas.
> >>>>
> >>>> Best,
> >>>> João
> >>>>
> >>>> --
> >>>> Attached Table 3
> >>>> met - method used, anl=analytical method, num=numerical method (DCLM)
> >>>> dots - number of points used for the numerical method
> >>>> src - source of the data, paper=Eisenhaber1995, ASC=ASC software,
> >>>> g463{sp,fx}=g_sas of GMX4.6.3 {single precision,fix
> >>>> 3199<https://gerrit.gromacs.org/#/c/3199/>
> >>>>
> >>>> }
> >>>> pbc - PBC flag for g_sas, yes=-pbc, no=-nopbc
> >>>> Areas are in square angstrom
> >>>> ======================================================
> >>>> met dots src pbc 4PTI 3FXN 1TIM
> >>>> ======================================================
> >>>> anl paper 3973.80 6943.80 20002.80
> >>>> anl ASC 3973.81 6943.80 20002.80
> >>>>
> >>>> num 122 paper 3961.40 6968.30 19970.90
> >>>> num 122 ASC 3961.44 6968.33 19970.90
> >>>> num 122 g463sp yes 3825.86 6257.83 19867.90
> >>>> num 122 g463sp no 4169.21 7731.63 24080.20
> >>>> num 122 g463fx yes 3825.86 6257.83 19867.90
> >>>> num 122 g463fx no 3957.81 6955.99 20004.20
> >>>>
> >>>> num 362 paper 3971.80 6933.40 19997.10
> >>>> num 362 ASC 3971.79 6933.37 19997.10
> >>>> num 362 g463sp yes 3838.35 6248.43 19886.80
> >>>> num 362 g463sp no 4195.02 7704.70 24132.10
> >>>> num 362 g463fx yes 3838.35 6248.43 19886.80
> >>>> num 362 g463fx no 3969.92 6936.20 20016.70
> >>>>
> >>>> num 642 paper 3967.90 6944.40 19998.70
> >>>> num 642 ASC 3967.78 6944.37 19998.70
> >>>> num 642 g463sp yes 3831.64 6255.64 19882.70
> >>>> num 642 g463sp no 4188.63 7701.99 24119.40
> >>>> num 642 g463fx yes 3831.64 6255.64 19882.70
> >>>> num 642 g463fx no 3966.21 6941.26 20013.60
> >>>>
> >>>> num 1002 paper 3974.10 6939.10 20012.20
> >>>> num 1002 ASC 3974.07 6939.12 20012.20
> >>>> num 1002 g463sp yes 3840.58 6250.14 19897.40
> >>>> num 1002 g463sp no 4193.60 7700.64 24143.10
> >>>> num 1002 g463fx yes 3840.58 6250.14 19897.40
> >>>> num 1002 g463fx no 3973.51 6939.68 20027.50
> >>>>
> >>>> num 1472 paper 3975.70 6943.30 19997.00
> >>>> num 1472 ASC 3975.70 6943.35 19996.90
> >>>> num 1472 g463sp yes 3841.69 6256.92 19882.80
> >>>> num 1472 g463sp no 4198.08 7709.30 24123.30
> >>>> num 1472 g463fx yes 3841.69 6256.92 19882.80
> >>>> num 1472 g463fx no 3975.88 6943.96 20012.40
> >>>> ======================================================
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Fri, Feb 28, 2014 at 4:49 AM, Teemu Murtola <
> teemu.murtola at gmail.com
> >>>> >wrote:
> >>>>
> >>>> Hi,
> >>>>>
> >>>>> On Thu, Feb 27, 2014 at 4:09 PM, Teemu Murtola <
> >>>>> teemu.murtola at gmail.com
> >>>>>
> >>>>>> wrote:
> >>>>>>
> >>>>>
> >>>>> I'll post additional information once I have had time to test more
> >>>>>> cases.
> >>>>>>
> >>>>>>
> >>>>> I have now created <http://redmine.gromacs.org/issues/1445> to track
> >>>>> the
> >>>>> issue, and uploaded a fix to Gerrit: <https://gerrit.gromacs.org/#/
> >>>>> c/3199/
> >>>>>
> >>>>>> .
> >>>>>>
> >>>>> My current set of tests is here: <
> https://gerrit.gromacs.org/#/c/3200/
> >>>>> >
> >>>>>
> >>>>> Looking at the history, as described in the Redmine issue, this
> should
> >>>>> explain incorrect results with -nopbc. The Redmine issue also
> provides
> >>>>> an
> >>>>> explanation for why 4.0.4 gives the same results with -pbc and
> -nopbc.
> >>>>> This
> >>>>> doesn't explain why it gives a slight underestimation with -pbc in
> >>>>> 4.6.3,
> >>>>> but you could try repeating the tests with the fixed version to see
> >>>>> whether
> >>>>> the PBC treatment or something else is giving rise to the
> >>>>> underestimation.
> >>>>>
> >>>>> Best regards,
> >>>>> Teemu
> >>>>> --
> >>>>> Gromacs Users mailing list
> >>>>>
> >>>>> * Please search the archive at
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> >>>>> posting!
> >>>>>
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> >>>>>
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> >>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>> --
> >>> David van der Spoel, Ph.D., Professor of Biology
> >>> Dept. of Cell & Molec. Biol., Uppsala University.
> >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> >>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
> >>> --
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> >>>
> >>
> >>
> >>
> >> --
> >> João M. Damas
> >> PhD Student
> >> Protein Modelling Group
> >> ITQB-UNL, Oeiras, Portugal
> >> Tel:+351-214469613
> >>
> >
> >
> >
> > --
> > João M. Damas
> > PhD Student
> > Protein Modelling Group
> > ITQB-UNL, Oeiras, Portugal
> > Tel:+351-214469613
> >
>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
>
> --
> Gromacs Users mailing list
>
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