AMBER Archive (2009)

Subject: [AMBER] sander.MPI and pmemd.MPI in Fedora 8

From: John Bennett (
Date: Sun Mar 15 2009 - 16:23:16 CDT

Dear Amber Users,
I'm now using just sander ( serial mode in Amber 10 ) in Fedora 8 . I also want to use SANDER and PMEMD in paralell mode with MPI ( sander.MPI and pmemd.MPI ). I think that I should seperately install PMEMD for Amber 10. Because when I write the command to run a md in serial mode like '' pmemd -O -i -o md_classical.out -p NMA.prmtop -c min_classical.rst -r md_classical.rst -x md_classical.mdcrd'' I see pmemd : command not found . I have not enough info about installing pmemd. So I need the users help who successfuly run pmemd and pmemd.MPI in Amber. My pc details are : "Intel CoreQuad 2.4 GHz, 1066 MHz CPU, Gigabyte SC-775 motherboard, Kingston 2 GB 1066 MHz HyperX Memory, Samsung 7200 RPM 500 GB SATA-II HDD, ASUS 512 MB 8600GT 128 Bit PCI-Ex display card’’ So Can I use  sander.MPI and pmemd.MPI in my pc ? If so, Could you help me to install pmemd and also run sander.MPI and pmemd.MPI in pc ?
Thanks in advance,
Kind Regards,

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