Hello Prof David Case
I had been running the system with dt=0.001. However, after 1ns
simulation when I increased dt to 0.002fs, it crashed with the
following error:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 5407 8261 8262
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
However I could not observe anything weird on VMD for atoms 8261 and 8262
How do I solve this problem? Which input files do I need to send?
Thanks for all your help
Debostuti
On Sat, May 19, 2012 at 11:44 PM, DEBOSTUTI GHOSHDASTIDAR
<debostutighosh.gmail.com> wrote:
>
> I am running the system in parallel
>
>
> On Sat, May 19, 2012 at 11:43 PM, DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com> wrote:
>>
>> Hi
>>
>> The moment I change to dt=.001 there is no more problem, the system runs...following is my input for the NPT step that failed
>>
>> NPT . 298K,
>> &cntrl
>> imin = 0, ntx = 7, irest = 1,
>> ntpr = 1, ntwx = 1, ntwe = 0,
>> ntc = 2, ntf = 2,iwrap=1,
>> nstlim = 1000, dt =0.002,
>> tempi=298.0, temp0 = 298.0, ntt =1, tautp =2.0,
>> ntb = 2, ntp = 1, taup = 3.0, pres0 =1.0,
>> &end
>>
>> Thanks for all your help
>>
>>
>>
>>
>>
>> On Sat, May 19, 2012 at 6:48 PM, case <case.biomaps.rutgers.edu> wrote:
>>>
>>> On Sat, May 19, 2012, DEBOSTUTI GHOSHDASTIDAR wrote:
>>> >
>>> > Following are the last few steps from the out file. I ran with
>>> > taup=3....the error file shows "forrtl: severe (174): SIGSEGV,
>>> > segmentation fault occurred" ...
>>>
>>> Sorry for the truncated earlier email. It's not clear that pressure has
>>> anything to do with the problem, but you might try setting dt=0.001 and even
>>> taup=30. to see what happens. What value of ntt (and other thermostat
>>> parameters) are you using? Are you running on a GPU? in parallel?
>>>
>>> It's a rather odd error, and I'm grasping at straws to find a clue. We will
>>> probably have to get your input files to see if the problem is reproducible.
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
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>>
>>
>>
>>
>> --
>> Debostuti
>>
>
>
>
> --
> Debostuti
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Received on Mon Jun 18 2012 - 07:00:03 PDT
