[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)
João M. Damas
jmdamas at itqb.unl.pt
Wed Mar 5 11:05:52 CET 2014
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
>>>>>
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>>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> 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
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