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

Tue Jun 21 09:29:51 CEST 2016

Thank you David! :)

On 21 June 2016 at 17:24, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> On 21/06/16 08:54, Billy Williams-Noonan wrote:
>
>> Thanks for your reply, I think this is helping.
>>
>>    Using your equation above I would need about 82TB for 1000 frames...
>>  I
>> somehow feel that this would be inaccessible for any calculation using
>> just
>> one node, which is a requirement for g_covar.
>>
> That would be an expensive computer.
>
> I could reduce the frames but I think I would wind up sub-sampling my
>> system.
>>
>>    I am selecting the entire system twice in gmx covar to get the entropy
>> of the system in gmx anaeig (as shown in the command on the original
>> post).  Are you saying I should just select the protein, ligand and
>> complex
>> for each ensemble?
>>
> Yes, this is what is typically done. Periodic boundary conditions would
> otherwise make the calculation miserable too.
>
>
>> Billy
>>
>>
>>
>> On 21 June 2016 at 16:39, 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
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>>>>>> 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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