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

[Qasim Pars]

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?

Why 4 bytes?

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
>>>> --
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>>> 
>>> 
>>> 
>>> --
>>> 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
> -- 
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