Hi
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
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!
> _______________________________________________
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> 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
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Received on Tue Aug 11 2015 - 12:00:02 PDT
