[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 03:27:32 CET 2014
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
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