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

[Billy Williams-Noonan]

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.
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?

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
>>>> --
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>>>>
>>>
>>>
>>> --
>>> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>>>
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>>> <
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>>> >
>>> **|*   +61420 382 557
>>>
>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
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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
> --
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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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Royal Parade, Parkville, 3052