[gmx-users] Cannot allocate memory problem during genion

sunita at chem.iitb.ac.in sunita at chem.iitb.ac.in
Fri Mar 3 06:28:22 CET 2006

Dear users,

I am trying to perform MD on a very big system consisting of 3391469
atoms. The net charge of the system is 10. So I wanted to add counterions
to make the system neutral. While perfoming genion I got following error
'cannot allocate memory'. The machine where I performed genion has 1 GB of
RAM. Will it be insufficient to work in a bigger system?

How to solved this problem?

Your suggestions will be appreciated.

------------------------error msg.-------------------------------
Select a group: 12
Selected 12: 'SOL'
Number of (3-atomic) solvent molecules: 1130021
Doing single force calculation...
Fatal error: realloc for nlist->jjnr (331939840 bytes, file ns.c, line
368, nlist->jjnr=0x0x186f3a20): Cannot allocate memory

with best regards,

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