lzheng at me.rochester.edu
Tue Nov 30 16:45:15 CET 2004
Thanks, David. The same configuration runs 100+ ps in DL_POLY, but I'll
check again if there are any conversion (from .xyz to pdb to gro)
How about my second question about dihedral potential? Thanks!
On Thu, 25 Nov 2004, David wrote:
>On Wed, 2004-11-24 at 16:30 -0500, Lianqing Zheng wrote:
>> Dear GMX-pals,
>> I try to run NPT MD simulation of RDX and got a segmentation error for
>> non-mpi version and "MPI process rank 0 (n0, p10908) caught a SIGSEGV."
>> error for lam/mpi version. This happens when PME is turned on. When I use
>> Cut-off, it gets stuck at step 5 and temperature becomes extremely high.
>sounds like a bad starting structure.
>> Another question is about dihedral entries. If there are repeated
>> entries, such as:
>> 1 2 3 4 1 180.0 10.0 2
>> 1 2 3 4 1 180.0 1.0 4
>> The results will be summation of these two or only the second?
>> Thanks a lot!
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>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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