Dear AMBER,
I¡¯m trying to benchmark the performance of AMBER and GMD (a GPU enabled MD program) in simulation of a PE (polyethylene) system with (298 CH2 + 2 CH3) united atoms*150, 45,000 atoms in total.
I got the following error at the first run by sander -O -i mdin -o mdout -c 45000.inpcrd -p 45000.prmtop.
*** glibc detected *** /home/nfsdata/installed-software/amber12/bin/sander: free(): invalid next size (normal): 0x000000001d45f570 ***
And the contents of the mdout file are just as follows:
------------------------------------------------------
Amber 12 SANDER 2012
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The AMBER input files(45000.inpcrd, 45000.prmtop) for the PE MD simulation are created by my own according to the file format of AMBER, not generated by xleap or other tools. So I think the error may be caused by the improper input files. I have checked the input files with much care, but can not work out.
It would be a great help for me if you help me to find the error in the AMBER input files (45000.inpcrd, 45000.prmtop, mdin). Please find them in the attached file.
By the way, I have another question that if VMD supports the conversion from GROMACS input to AMBER input file format.
Thank you for your attention. I¡¯m looking forward to your early reply.
--
Best regards£¡
Xiaofang Tao
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Received on Wed Apr 24 2013 - 18:30:25 PDT
