[gmx-users] Schlitter Configurational entropy 'NaN'
tarak karmakar
tarak20489 at gmail.com
Thu May 15 18:41:42 CEST 2014
Hi Justin,
That's true and it is a C code and 0 index loop.
Then the strange jump 999 to 1000 came in to the picture.
But what about dealing with very small numbers?
Tarak
On Thu, May 15, 2014 at 9:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/15/14, 11:51 AM, tarak karmakar wrote:
>
>> Part of the eigenval.xvg file
>>
>> 995 3.02979e-06
>> 996 2.98051e-06
>> 997 2.93131e-06
>> 998 2.75594e-06
>> 999 2.69955e-06
>> 1000 2.56434e-06
>> 1001 2.66401e-16
>> 1002 1.43252e-16
>> 1003 1.0735e-16
>> 1004 8.0728e-17
>> 1005 4.3465e-17
>> 1006 1.60571e-17
>> 1007 1.49006e-17
>> 1008 1.44694e-17
>> 1009 1.07083e-17
>> 1010 9.77564e-18
>> 1011 8.25739e-18
>> 1012 8.18473e-18
>> 1013 6.85267e-18
>> 1014 6.79135e-18
>> 1015 5.7498e-18
>> 1016 5.49917e-18
>> 1017 4.84525e-18
>> 1018 4.15989e-18
>> 1019 4.06407e-18
>> 1020 3.70677e-18
>> .............................
>> .............................
>> 1362 -3.16429e-18
>> 1363 -3.40673e-18
>> 1364 -3.85766e-18
>> 1365 -4.16796e-18
>> 1366 -4.16839e-18
>> 1367 -4.17689e-18
>> 1368 -4.48977e-18
>> 1369 -4.54731e-18
>> 1370 -4.58794e-18
>> 1371 -4.86076e-18
>> 1372 -5.05864e-18
>> 1373 -5.73908e-18
>> 1374 -6.1385e-18
>> 1375 -6.98907e-18
>> 1376 -7.5897e-18
>> 1377 -1.23406e-17
>> 1378 -1.24701e-17
>> 1379 -1.41182e-17
>> 1380 -1.47709e-17
>> 1381 -1.50144e-17
>> 1382 -5.73596e-17
>> 1383 -1.03466e-16
>> 1384 -1.277e-16
>> 1385 -1.64873e-16
>> 1386 -3.2657e-16
>>
>> These eigenvalues are very less compared to the below 1000 numbers.
>> I see there is no strange jump from 999 to 1000 but from 1000 to 1001.
>>
>>
> The array in the code is zero-indexed, so this is actually the location of
> the problem.
>
> -Justin
>
>
> Lambda values are considered to be zero in these cases and thus
>> w = sqrt(BOLTZMANN*temp/lambda)/NANO = infinity
>> &
>> dd = 1+kteh*eigval[i];
>> deter += log(dd)
>> is failed.
>>
>> i = 1000 w = inf lam = 0 hwkT = inf dS =
>> -nan
>> i = 1001 w = inf lam = 0 hwkT = inf dS =
>> -nan
>> i = 1002 w = inf lam = 0 hwkT = inf dS =
>> -nan
>>
>> So, there is precision problem in the code; 10^-16 is taken as zero!!
>>
>> Tarak
>>
>>
>>
>>
>> On Thu, May 15, 2014 at 5:23 PM, David van der Spoel
>> <spoel at xray.bmc.uu.se>wrote:
>>
>> On 2014-05-15 11:40, tarak karmakar wrote:
>>>
>>> Dear Sir,
>>>>
>>>> Thank you again for guiding me towards this. Got some clue.
>>>> The g_anaeig code is
>>>> ............................................................
>>>> ............................................................
>>>> .................
>>>> static void calc_entropy_qh(FILE *fp,int n,real eigval[],real temp,int
>>>> nskip)
>>>> {
>>>> int i;
>>>> double hwkT,w,dS,S=0;
>>>> double hbar,lambda;
>>>>
>>>> hbar = PLANCK1/(2*M_PI);
>>>> for(i=0; (i<n-nskip); i++) {
>>>> if (eigval[i] > 0) {
>>>> lambda = eigval[i]*AMU;
>>>> w = sqrt(BOLTZMANN*temp/lambda)/NANO;
>>>> hwkT = (hbar*w)/(BOLTZMANN*temp);
>>>> dS = (hwkT/(exp(hwkT) - 1) - log(1-exp(-hwkT)));
>>>> S += dS;
>>>> if (debug)
>>>> fprintf(debug,"i = %5d w = %10g lam = %10g hwkT = %10g dS =
>>>> %10g\n",
>>>> i,w,lambda,hwkT,dS);
>>>> }
>>>> else {
>>>> fprintf(stderr,"eigval[%d] = %g\n",i,eigval[i]);
>>>> w = 0;
>>>> }
>>>> }
>>>> fprintf(fp,"The Entropy due to the Quasi Harmonic approximation is
>>>> %g
>>>> J/mol K\n",
>>>> S*RGAS);
>>>> }
>>>>
>>>> static void calc_entropy_schlitter(FILE *fp,int n,int nskip,
>>>> real *eigval,real temp)
>>>> {
>>>> double dd,deter;
>>>> int *indx;
>>>> int i,j,k,m;
>>>> char buf[256];
>>>> double hbar,kt,kteh,S;
>>>>
>>>> hbar = PLANCK1/(2*M_PI);
>>>> kt = BOLTZMANN*temp;
>>>> kteh = kt*exp(2.0)/(hbar*hbar)*AMU*(NANO*NANO);
>>>> if (debug)
>>>> fprintf(debug,"n = %d, nskip = %d kteh = %g\n",n,nskip,kteh);
>>>>
>>>> deter = 0;
>>>> for(i=0; (i<n-nskip); i++) {
>>>> dd = 1+kteh*eigval[i];
>>>> deter += log(dd);
>>>> }
>>>> S = 0.5*RGAS*deter;
>>>>
>>>> fprintf(fp,"The Entropy due to the Schlitter formula is %g J/mol
>>>> K\n",S);
>>>> }
>>>> ............................................................
>>>> ..............................................................
>>>> What I got from the 'g_anaeig_d.debug' file is given below
>>>>
>>>> i = 0 w = 1.06303e+12 lam = 3.66537e-27 hwkT = 0.0270659 dS =
>>>> 4.60951
>>>> i = 1 w = 1.50699e+12 lam = 1.82384e-27 hwkT = 0.0383696 dS =
>>>> 4.26055
>>>> i = 2 w = 1.62965e+12 lam = 1.55961e-27 hwkT = 0.0414928 dS =
>>>> 4.18231
>>>> i = 3 w = 2.02202e+12 lam = 1.01306e-27 hwkT = 0.0514829 dS =
>>>> 3.96662
>>>> i = 4 w = 2.80273e+12 lam = 5.27285e-28 hwkT = 0.0713605 dS =
>>>> 3.64022
>>>> i = 5 w = 3.1712e+12 lam = 4.11871e-28 hwkT = 0.0807422 dS =
>>>> 3.51677
>>>> i = 6 w = 3.45782e+12 lam = 3.46419e-28 hwkT = 0.0880401 dS =
>>>> 3.43029
>>>> i = 7 w = 3.56568e+12 lam = 3.25778e-28 hwkT = 0.0907862 dS =
>>>> 3.39959
>>>> i = 8 w = 4.00962e+12 lam = 2.57633e-28 hwkT = 0.102089 dS =
>>>> 3.28234
>>>> i = 9 w = 4.4611e+12 lam = 2.08125e-28 hwkT = 0.113584 dS =
>>>> 3.17575
>>>> i = 10 w = 4.6037e+12 lam = 1.95431e-28 hwkT = 0.117215 dS =
>>>> 3.14431
>>>> i = 11 w = 5.01062e+12 lam = 1.64977e-28 hwkT = 0.127576 dS =
>>>> 3.05972
>>>> i = 12 w = 5.31327e+12 lam = 1.46718e-28 hwkT = 0.135282 dS =
>>>> 3.00116
>>>> i = 13 w = 5.51169e+12 lam = 1.36345e-28 hwkT = 0.140334 dS =
>>>> 2.96455
>>>> i = 14 w = 5.70613e+12 lam = 1.27211e-28 hwkT = 0.145284 dS =
>>>> 2.92994
>>>> i = 15 w = 5.8637e+12 lam = 1.20466e-28 hwkT = 0.149296 dS =
>>>> 2.90275
>>>> i = 16 w = 6.01592e+12 lam = 1.14447e-28 hwkT = 0.153172 dS =
>>>> 2.87717
>>>> ----------------------
>>>> .......................
>>>> i = 996 w = 9.2246e+14 lam = 4.86757e-33 hwkT = 23.4869 dS =
>>>> 1.54425e-09
>>>> i = 997 w = 9.51359e+14 lam = 4.57635e-33 hwkT = 24.2226 dS =
>>>> 7.62131e-10
>>>> i = 998 w = 9.61243e+14 lam = 4.48271e-33 hwkT = 24.4743 dS =
>>>> 5.98465e-10
>>>> i = 999 w = 9.86259e+14 lam = 4.25819e-33 hwkT = 25.1113 dS =
>>>> 3.2445e-10
>>>> i = 1000 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1001 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1002 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> ......................
>>>> ..................
>>>> i = 1370 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1371 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1372 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1373 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1374 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1375 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1376 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1377 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1378 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> i = 1379 w = inf lam = 0 hwkT = inf dS =
>>>> -nan
>>>> n = 1386, nskip = 6 kteh = 4569.58
>>>> Opening library file /usr/share/gromacs/top/gurgle.dat
>>>>
>>>>
>>>> It is very interesting that the code printed 'nan' after 999 th term.
>>>> What
>>>> does this mean?
>>>> Is there any upper limit of number of atoms (c-alpha here)?
>>>>
>>>> Check your eigval.xvg file, what is the value at i = 1000?
>>> It seems that lambda is the problem, hence I suspect the eigval[1000] to
>>> be strange.
>>>
>>>
>>> Tarak
>>>>
>>>>
>>>>
>>>> On Thu, May 15, 2014 at 2:54 PM, David van der Spoel
>>>> <spoel at xray.bmc.uu.se>wrote:
>>>>
>>>> On 2014-05-15 10:51, tarak karmakar wrote:
>>>>
>>>>>
>>>>> | Is your system far out of equilibrium?
>>>>>
>>>>>>
>>>>>> It should not be as I have simulated the system for 100ns. Few
>>>>>> properties
>>>>>> to check to get the feelings of equilibrium are looking good.
>>>>>>
>>>>>> |Do the eigenvalues look reasonable?
>>>>>> Yes. File is attached.
>>>>>>
>>>>>> | Or is your system very large?
>>>>>> My system is a protein dimer.
>>>>>>
>>>>>> It creates the following covariance matrix (c-alpha atoms)
>>>>>>
>>>>>> Constructing covariance matrix (1386x1386)
>>>>>>
>>>>>> That is big.
>>>>>>
>>>>>
>>>>> Try running g_anaeig -debug 1 and check the output file g_anaeig.debug.
>>>>> Then check the source code (gmx_anaeig.c) to see whether the evaluation
>>>>> of
>>>>> the entropy can be made more numerically stable.
>>>>>
>>>>>
>>>>> eigenvec.trr file is also attached.
>>>>>
>>>>>>
>>>>>> Mail with the attached files
>>>>>> "Needs moderator approval because of the file size."
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>> Tarak
>>>>>>
>>>>>>
>>>>>> On Thu, May 15, 2014 at 2:19 PM, tarak karmakar <tarak20489 at gmail.com
>>>>>>
>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>> | Is your system far out of equilibrium?
>>>>>>
>>>>>>
>>>>>>> It should not be as I have simulated the system for 100ns. Few
>>>>>>> properties
>>>>>>> to check to get the feelings of equilibrium are looking good.
>>>>>>>
>>>>>>> |Do the eigenvalues look reasonable?
>>>>>>> Yes. File is attached.
>>>>>>>
>>>>>>> | Or is your system very large?
>>>>>>> My system is a protein dimer.
>>>>>>>
>>>>>>> It creates the following covariance matrix (c-alpha atoms)
>>>>>>>
>>>>>>> Constructing covariance matrix (1386x1386)
>>>>>>>
>>>>>>> eigenvec.trr file is also attached.
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Tarak
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, May 15, 2014 at 2:06 PM, David van der Spoel <
>>>>>>> spoel at xray.bmc.uu.se
>>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 2014-05-15 10:30, tarak karmakar wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Dear Sir,
>>>>>>>>
>>>>>>>> Thanks for the quick reply.
>>>>>>>>> Using g_anaeig_d I've got both of them as 'nan'
>>>>>>>>>
>>>>>>>>> The Entropy due to the Quasi Harmonic approximation is -nan J/mol K
>>>>>>>>> The Entropy due to the Schlitter formula is nan J/mol K
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Interesting. Is your system far out of equilibrium? Do the
>>>>>>>>>
>>>>>>>> eigenvalues
>>>>>>>> look reasonable? Or is your system very large?
>>>>>>>>
>>>>>>>>
>>>>>>>> Tarak
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, May 15, 2014 at 1:30 PM, David van der Spoel
>>>>>>>>> <spoel at xray.bmc.uu.se>wrote:
>>>>>>>>>
>>>>>>>>> On 2014-05-15 09:07, tarak karmakar wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Dear All,
>>>>>>>>>>
>>>>>>>>>> I wanted to calculate configurational entropy of a protein by
>>>>>>>>>> using
>>>>>>>>>>
>>>>>>>>>>> g_covar
>>>>>>>>>>> and g_anaeig as follows,
>>>>>>>>>>>
>>>>>>>>>>> g_covar -f ../traj.xtc -s ../npt_prod -o eigenval -v eigenvec.trr
>>>>>>>>>>> -av
>>>>>>>>>>> average.pdb
>>>>>>>>>>> g_anaeig -v eigenvec.trr -entropy -temp 300
>>>>>>>>>>>
>>>>>>>>>>> I got the following results
>>>>>>>>>>>
>>>>>>>>>>> The Entropy due to the Quasi Harmonic approximation is 31440.3
>>>>>>>>>>> J/mol
>>>>>>>>>>> K
>>>>>>>>>>> The Entropy due to the Schlitter formula is nan J/mol K
>>>>>>>>>>>
>>>>>>>>>>> I went back to check the eigenvector file by dumping it to a new
>>>>>>>>>>> file
>>>>>>>>>>> 'dump'. There is no 'nan' indeed.
>>>>>>>>>>>
>>>>>>>>>>> Could anyone comment on why I'm getting Schlitter entropy as
>>>>>>>>>>> 'nan'?
>>>>>>>>>>>
>>>>>>>>>>> Thanks and regards,
>>>>>>>>>>> Tarak
>>>>>>>>>>>
>>>>>>>>>>> Numerical error due to large numbers. Try compiling gromacs
>>>>>>>>>>> in
>>>>>>>>>>> double
>>>>>>>>>>>
>>>>>>>>>>> precision.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>>
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>>>>>>>>>>
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>>>>>>>>>> gmx-usersor
>>>>>>>>>> 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
>>>>>>>> --
>>>>>>>> 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
>>>>> --
>>>>> 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
>>> --
>>> Gromacs Users mailing list
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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