[gmx-users] Schlitter Configurational entropy 'NaN'

[tarak karmakar]

 | 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.

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
>>>> --
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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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-- 







*Tarak KarmakarMolecular Simulation Lab.Chemistry and Physics of Materials
UnitJawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O.
Bangalore - 560 064Karnataka, INDIAPh. (lab) : +91-80-22082809 *