[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)
João M. Damas
jmdamas at itqb.unl.pt
Tue Mar 4 17:05:56 CET 2014
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
>>> --
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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
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