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

[David van der Spoel]

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