Hi,
Have you been able to run any of the test cases? Do you get the same error?
-Dan
On Wed, Apr 24, 2013 at 7:19 PM, 陶晓芳 <xftao.home.ipe.ac.cn> wrote:
> 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
> -------------------------------------------------------
>
> 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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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Apr 25 2013 - 08:00:03 PDT
