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

Tue Jun 21 09:24:58 CEST 2016

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
>>>>>
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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
>> --
>> 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