[gmx-users] Range checking error

Yanzi Zhou 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 
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 

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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