[gmx-users] Problem with gmx clustsize ..(Not enough memory. Failed to calloc)

David van der Spoel spoel at xray.bmc.uu.se
Mon May 14 19:55:33 CEST 2018

Den 2018-05-14 kl. 12:40, skrev Sergio Garay:
> Thank you Mark for your answer! I have also tried to run clustsize
> using different dt, from 1 ns to 10ns (the trajectory only have 10
> frames) but it still give the same error, so I think that I am doing
> something wrong. May be the problem is the way the program identify
> each molecule.
Try using an index file leaving out the water.
> Thank you very much, I will keep trying to solve this problem.
> Sergio
>> Hi,
>> Clustering requires that you build a matrix in memory that contains the
>> difference between each structure you intend to cluster. If you e.g. use
>> every frame from your trajectory, then you will typically exhaust the
>> available memory, as here. Reconsider how you will find out the period
>> between statistically independent observations, and (if needed once you
>> have done the former) access a node with more memory.
>> Mark
>> On Sat, May 12, 2018 at 4:18 PM Sergio Garay <sergio.alberto.garay at gmail.com <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
>> wrote:
>> * Dear Gromacs users
> *>>* I am trying to analyse a MD simulation of 30 lipopeptides in water, in
> *>* particular I would like to obtain the average number of these molecules in
> *>* each assembly, along the time. I have tried g_clustsize with my simulation
> *>* box with only the lipopeptides. For that I prepared a tpr file for these
> *>* molecules only. But I have these error:
> *>>* *g_clustsize -f 0-100ns.xtc -s micelle-alone.tpr -nc -mol -dt 1000*
> *>>* Fatal error:
> *>* Not enough memory. Failed to calloc -1082130432 elements of size 4 for
> *>* grps[j].nm_ind
> *>* (called from file
> *>* /home/sgaray/Programas/gromacs-5.0.4/src/gromacs/fileio/tpxio.c,
> *>* line 2510)
> *>>* Could someone tell me what I am doing wrong?
> *>>* Thank you in advance.*

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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