[gmx-users] Schlitter Configurational entropy 'NaN'
tarak karmakar
tarak20489 at gmail.com
Thu May 15 12:02:28 CEST 2014
To add the previous post.
I took a small fraction of the protein (a loop), follow the same protocol,
and got the results.
The Entropy due to the Quasi Harmonic approximation is 2814 J/mol K
The Entropy due to the Schlitter formula is 3000.03 J/mol K
Regarding the g_anaeig.c code, do we need to increase the precision of all
the floating point numbers, say from 'double' to 'long double'?
Tarak
On Thu, May 15, 2014 at 3:10 PM, tarak karmakar <tarak20489 at gmail.com>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)?
>
> 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
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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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>>>>> * Please search the archive at http://www.gromacs.org/
>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
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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
>>
>> * 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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