Hi,
Your coordinates have overflowed. It is recommended that when running
simulations with PBC you turn on coordinate wrapping (iwrap = 1) to
prevent this. If you are using Amber12 you can also try using the new
NetCDF restart file format (ntxo = 2) which has higher precision than
ASCII restarts.
-Dan
On Thu, Jul 12, 2012 at 12:17 PM, Ashutosh Shandilya
<izerokelvin.gmail.com> wrote:
>> I restarted my simulation again this time in explicit solvent but after
>> running 210 ns it again shows the same problem that it could not read the
>> coordinates. I tried with so many different ways is there any way to
>> restart my job. I have attached the topology and restart file which has
>> problem and the input file as well.
>> Kindly have a look.
>>
>> Thanks
>>
>>
>>
>> On 21 June 2012 17:09, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>> This is happening because the coordinates are overflowing, either
>>> because the system is massive or part of it has moved far away from
>>> the coordinate origin. Not knowing the specifics of your system I
>>> can't be sure, but it appears that this problem is with the last atom
>>> in your system, which appears to be very far away from everything else
>>> for some reason. If you are using Amber12 you can use the new netcdf
>>> restart file format (ntxo = 2, see http://ambermd.org/doc12/ for a
>>> little more info) which can hold larger numbers than the ASCII restart
>>> format. Note that netcdf restarts are currently only supported by
>>> Amber12 sander, pmemd, cpptraj, and NAB.
>>>
>>> -Dan
>>>
>>> On Wed, Jun 20, 2012 at 3:34 PM, Ashutosh Shandilya
>>> <izerokelvin.gmail.com> wrote:
>>> > Dear Amber users
>>> >
>>> > The coordinate file after simulation (implicit) is showing star mark
>>> > highlighted in the first column. I reran the simulation but again it
>>> shows
>>> > the same error and one more observation was that the (x,y,z) coordinate
>>> > values are quite high from the original one. To generate a pdb file if I
>>> > manually give some arbitrary similar value instead of stars and again
>>> > restart the simulation its giving nan values.
>>> >
>>> > 1184.6077849 87.8888422 467.84796201185.3934567 87.3155358 466.8924446
>>> > 1185.2680706 88.7090605 464.54429731186.4476164 89.0831923 464.6623140
>>> > 1184.8475718 87.6484031 463.75189751183.8646739 87.4420910 463.7650775
>>> > 1185.7071448 86.8318350 462.86466941185.0671587 86.3891983 462.1111381
>>> > 1186.3153669 87.5821378 462.35431881186.6158655 85.8276403 463.4688349
>>> > 1187.5664425 85.4647477 462.72178371186.3922755 85.4288019 464.6323917
>>> > ************* *-48.0818384-390.5949655
>>> > 0.0068848 0.0591804 -0.1366963 1.8340742 -0.6580615 -0.6321001
>>> > -0.6970049 0.0615980 -0.9000795 1.2015969 0.2187631 -0.5411940
>>> > 0.1566680 0.3761406 -0.5256694 -0.7715472 -1.1329467 -0.3315136
>>> > 0.8764598 0.0811084 1.0273480 0.2398398 -0.1928732 -0.0443124
>>> > -0.0285152 0.3707692 -0.1225974 -0.0579449 -0.2956305 -0.2325728
>>> > 0.4026198 0.3070977 0.2775148 -0.3166358 -0.2877791 0.1805477
>>> >
>>> > If some one came across this problem and have any clue that would help.
>>> > Thanks
>>> > Ashutosh
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Lab Specialist
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 201
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-9119 (Fax)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Jul 13 2012 - 11:30:03 PDT
