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

Tue Jun 21 10:25:20 CEST 2016

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)

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
>>>
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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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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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<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