[gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Tue Jun 21 11:17:07 CEST 2016

On 21/06/16 10:25, Billy Williams-Noonan wrote:
> A related problem, when I compute the entropy for:
>
> <dS> = <S(complex)> - <S(ligand)> - <S(protein)>
>
> I get a T<dS> of -8640 kJ/mol (or <dS>=-28.9 kJ/mol/K)
>
Unit for S is J/mol K.

> This value seems inordinately high...
>
> If T<dS> was actually -28.9 kJ/mol that would match well with experimental
> data given my enthalpy.
>
> I am selecting the relevant biomolecule for each ensemble.  This seems
> unlikely to be a convergence problem...
>
> Billy
>
> On 21 June 2016 at 17:52, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
>> On 21/06/16 09:40, Qasim Pars wrote:
>>
>>> Dear David,
>>>
>>> Could you please more explain each term of the formula you said?
>>>
>>> Formula=The number of atoms (N * 3)^2 times number of frames times 4 bytes
>>>
>>> Why square the number of atoms?
>>>
>> Because we build a matrix of all degrees of freedom.
>>
>>>
>>> Why 4 bytes?
>>>
>> The size of a floating point number. Unless you built gromacs in double
>> precision.
>>
>>
>>> Thanks in advance
>>>
>>> On 21 Jun 2016, at 09:39, David van der Spoel <spoel at xray.bmc.uu.se>
>>>> wrote:
>>>>
>>>> On 21/06/16 08:11, Billy Williams-Noonan wrote:
>>>>>   Sorry, the original post provides an example of the -dt flag with
>>>>> 100ps
>>>>> intervals.
>>>>>
>>>> You can calculate how much space you need by number of atoms (N * 3)^2
>>>> times number of frames times 4 bytes.
>>>>
>>>> Do you select just your biomolecule?
>>>>
>>>>
>>>>> On 21 June 2016 at 16:10, Billy Williams-Noonan <
>>>>> billy.williams-noonan at monash.edu> wrote:
>>>>>
>>>>> Thank you for your reply. :)
>>>>>>
>>>>>>   My main problem is with gmx covar which does not have a -skip flag.
>>>>>> As
>>>>>> you can see from the OP I have tried the -dt flag with 250ps
>>>>>> intervals.  It
>>>>>> still crashes due to insufficient memory.  It also crasses with 5000ps
>>>>>> intervals, giving me just 20ps of frames to work with for the whole
>>>>>> ensemble.
>>>>>>
>>>>>> Billy
>>>>>>
>>>>>> On 21 June 2016 at 16:00, David van der Spoel <spoel at xray.bmc.uu.se>
>>>>>> wrote:
>>>>>>
>>>>>> On 21/06/16 07:34, Billy Williams-Noonan wrote:
>>>>>>>>
>>>>>>>> Hi Gromacs Users,
>>>>>>>>
>>>>>>>>   I am running g_mmpbsa.py to calculate the binding enthalpy of a
>>>>>>>> cyclic
>>>>>>>> peptide in a drug target.  At the same time I am trying to generate
>>>>>>>> ensemble estimates for entropy for the protein, ligand and complex.
>>>>>>>> By
>>>>>>>> using these two variables I aim to get an idea of the Gibbs free
>>>>>>>> energy
>>>>>>>> of
>>>>>>>> binding.
>>>>>>>>
>>>>>>>>   My system for the complex and the protein is some 50,000 atoms
>>>>>>>> large,
>>>>>>>> with just over 3000 atoms belonging to the proteins, and the rest of
>>>>>>>> the
>>>>>>>> system is water and ions, to make up a physiological concentration of
>>>>>>>> NaCl.  These are approximate estimates and not exact numbers.  gmx
>>>>>>>> covar
>>>>>>>> seems to keep crashing every time I try to use it to generate
>>>>>>>> eigenvectors
>>>>>>>> for the system.  These are the commands I am using:
>>>>>>>>
>>>>>>>>
>>>>>>>> "  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb
>>>>>>>> -ascii
>>>>>>>> covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100
>>>>>>>> -pbc
>>>>>>>> yes
>>>>>>>> << EOF
>>>>>>>> 0
>>>>>>>> 0
>>>>>>>> EOF  "
>>>>>>>>
>>>>>>>> and:
>>>>>>>>
>>>>>>>> "  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp
>>>>>>>> 300 >
>>>>>>>> out.entropy.schlitter  "
>>>>>>>>
>>>>>>>>
>>>>>>>>   I have tried this on a local machine with 16GB of RAM and on a
>>>>>>>> cluster
>>>>>>>> using one core and a node's worth of RAM (128GB).  I do not have
>>>>>>>> access
>>>>>>>> to
>>>>>>>> more RAM than this.  Any ideas on how I can stop my calculation from
>>>>>>>> crashing due to insufficient memory?
>>>>>>>>
>>>>>>> Use the -skip or -dt flags.
>>>>>>>
>>>>>>>
>>>>>>>   Kind regards,
>>>>>>>>
>>>>>>>>   Billy
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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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>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>>>>>>
>>>>>> *LinkedIn Profile
>>>>>> <
>>>>>> http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button
>>>>>>>
>>>>>> **|*   +61420 382 557
>>>>>>
>>>>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>>>>>> Royal Parade, Parkville, 3052
>>>>>>
>>>>>
>>>>
>>>> --
>>>> 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
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>>>>
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>>>>
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>>>> 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
>>
>> * Please search the archive at
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>> posting!
>>
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>>
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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