I did MD simulation for lipid. I downloaded the pre-equilibrated
structure and parameters from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I
can do 5 ns NTP simulation with single precision, but it can't go on
with double precision.
I also tried the DPPC from the benchmarks of Gromacs. I first did the
NTV simulation for 500 ps, and then do NTP simulation using PME, but
crashed.
Mark Abraham wrote:
Yanzi Zhou wrote:
Thank you.
I recompiled the software with gcc, but my job still crashed at about
170ps. I tried 1 ns simulation for 1PGB in water downloaded from
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be
finished. But when I tried to do NTP simulation of DPPC from the
benchmarks of Gromacs, my job died on 6 processes with double
precision gromacs. I found the job crashed when I:
do NTP simulation for a large system, and
use PME
on more than two processors with double precision gromacs.
Make sure your system is properly energy-minimized and that the
potential
energy seems reasonable before trying again.
What have you done to check that your system preparation protocol is
reasonable?
Mark
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