[gmx-users] Range checking error
yz30 at nyu.edu
Tue Nov 27 00:36:45 CET 2007
I did MD simulation for lipid. I downloaded the pre-equilibrated
structure and parameters from
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
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
>>>> energy seems reasonable before trying again.
> What have you done to check that your system preparation protocol is
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