did you look at the mdout file too? you want to make sure the simulation
did not have any problems other than this.
if you run long MD in GB with ntt=1, you are likely to have problems. This
is not really a good thermostat. That might not be the problem, but I would
certainly switch to the Langevin thermostat. Look for "flying ice cube"
references on the archive.
On Mon, Oct 31, 2016 at 2:34 PM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Dear Amber users,
>
> when I start the equilibration run after heating a protein molecule (about
> 200 aminoacid residues), I receive the error message:
>
> ERROR: Problem reading coordinates or velocities from
> EndoH1N1_gb_heat3slow.rst
>
> I could not understand line 1633 :
> 1525.3274188-173.5683801
> 718.8293045-836.78710421003.7855053************
>
>
> *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
>
> Here are the asterisks:
>
> 1525.7343256-173.6190120 719.0223153-837.01779391004.0492559************
> 679.4202985 9.14955061646.6762693 742.9513976************ 456.7156485
> -651.6670212 134.31713181725.18516571385.5565069************-822.2471921
>
>
> My input file for equilibration:
>
> Stage 4 equilibration of EndoH1N1 300K
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=50000, dt=0.001,
> ntc=2, ntf=2,
> nscm /= 0,
> ntt=1, tautp=1.0,
> tempi=300.0, temp0=300.0,
> ntpr=50, ntwx=50,
> ntb=0, igb=1,
> iwrap=1,
> cut=999.0,rgbmax=999.
> /
>
> the input file for the last heating stage:
>
> Stage 3 heating of EndoH1N1 200K to 300K
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=10000, dt=0.001,
> ntc=2, ntf=2,
> ntt=1, tautp=1.0,
> tempi=200.0, temp0=300.0,
> ntpr=50, ntwx=50,
> ntb=0, igb=1,
> iwrap=1,
> cut=999.0,rgbmax=999.
> /
>
> what should I change then?..
>
>
> Thank you in advance,
>
> Nick
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>
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Received on Mon Oct 31 2016 - 12:00:02 PDT
