From: Sridhar Kumar Kannam (
Date: Wed Apr 03 2013 - 18:03:55 CDT

Dear NAMD users.

I am working on tutorial - *Modeling Nanopores for Sequencing DNA.*

I increase the pore length and diameter and my new system contain around 3
million atoms. I am working on compressing the system using
genCompressedPsf to use NAMD memory reduction version. But I am getting the
error - FATAL ERROR: Memory allocation failed on processor 0.

The compression is working fine when I have only protein and water as the
I am having the problem when I have SiN (generated using inorganic builder)
or graphene (generated using nanotube builder) as a part of the system.

I have 16GB memory on the node I am using. The error is not really due to
the memory problem on the node but when I have SiN as a part of the system.

Can anyone please suggest me a way around ....

Thank you very much.

Cheers !!!
Sridhar  Kumar Kannam :)
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