On Tue, Aug 11, 2015 at 12:46 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Sorry to tell you , but you have a bigger problem. You are using the
> internal random seed for the langevin thermostat, while you should be
> using ig=-1
For more information see
http://pubs.acs.org/doi/abs/10.1021/ct8002173.
>
> I would not trust your results and would start over, using ig=-1 AND
> iwrap=1. Also, if you have netcdf, use ioutfm=1
>
> adrian
>
>
> On 8/11/15 1:18 PM, Amber mail wrote:
>> Dear AMBER users,
>>
>> Wish you are fine
>>
>> I performed a 80 ns MD simulation in 8 stages, using AMBER12, each stage
>> for 10 ns.
>>
>> *Description of the simulation:*
>>
>> I used this md control file for all stages
>>
>> Production
>> &cntrl
>> imin=0,
>> ntx=5,
>> irest=1,
>> nstlim=5000000,
>> dt=0.002,
>> ntf=2,
>> ntc=2,
>> temp0=310.0,
>> tempi=310.0,
>> ntpr=5000,
>> ntwx=5000,
>> cut=8.0,
>> ntb=2,
>> ntp=1,
>> ntt=3,
>> gamma_ln=1.0,
>> /
>>
>> *The Error*:
>>
>> 70 ns MD simulation was performed without any problems, but the 8th
>> stage(at 80 ns) failed due to this error below:
>>
>>> | ERROR: I could not understand line 8358
>>> 56.2239165************-423.4551515 56.1995897************-423.0909738
>>>
>>> *s in the inpcrd file often indicate an overflow of the Fortran format used
>>> to store coordinates in the inpcrd/restart files. This often happens when
>>> coordinates are not wrapped into the center cell (when iwrap = 0) and some
>>> particles diffuse too far away. Try restarting from your last good restart
>>> file and setting iwrap=1 or using a NetCDF restart file format. See the
>>> Amber manual for details
>>> "mol500008.out" 58L, 3283C
>>> 58,1 Bot
>>>
>>> I've checked the mailing list for a similar error, but It was not clear
>> enough for me.
>>
>>
>> *The question is:*
>>
>> Regarding the sentence from the mdout file, "Try restarting from your last
>> good restart file ", how can I know how good the restart file is? does this
>> simply mean a restart file from a completed stage?!
>>
>> Is the solution to this just by setting iwrap=1 and resume the 8th stage
>> using the restart file from the 7th stage, or I have to repeat all the MD
>> simulation with setting iwrap=1 ?!
>>
>> Does just setting iwrap=1 and resuming the simulation with the 8th stage
>> affect the results of the MD simulation?
>>
>> I also want to point out that I managing to run the MD simulation till 100
>> ns.
>>
>>
>> Thanks in advance!
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 11 2015 - 12:30:04 PDT
