try running with single processor (not parallel) and see if you get better
error information in the output. It could be that the error happened on a
cpu not writing to the output file, but the details of where to find the
error message can depend on your computer system setup.
On Thu, Jul 21, 2016 at 7:31 AM, 乔艳 <yanqiao.zzu.edu.cn> wrote:
> Dear amber users,
> I am using Amber16 to do a simulation for a complex. I first performed
> minimizations for the complex and everything is OK. However, when I want to
> equilibrate the water molecules and elevate the temperature of the system,
> the simulation can not proceed normally. There is no error information in
> the output file, but the simulation can not go on. Can any one help me?
> The script is as follows:
> $DO_PARALLEL sander.MPI -O -i mdw.in -o mdw.out -p
> 4NRE_solv.prmtop -c m4.rst -r mdw.rst -x mdw.mdcrd -ref
> m4.rst
>
> The mdw.in file is as follows:
> # Control section
> &cntrl
> nstlim=100000, dt=0.002, ntx=1, irest=0,ig=-1, ntpr=1000,
> ntwr=1000,ntwx=1000,
> tempi=10.15, temp0=298.15, ntt=1,tautp=2,
> ntb=1, ntp=0,
> ntc=2, ntf=2,
> cut=10.0,
> ntr=1, restraintmask=':1-675',
> restraint_wt=5.0,
> &end
> &ewald
> &end
>
> The mdw.out file is as follows and there is no error information.
>
> ***************
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> | # of SOLUTE degrees of freedom (RNDFP): 194726.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 194726. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> 194726.
> | TOTAL # of degrees of freedom (RNDF) = 194726.
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
>
>
> _______________________________________________
> 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
Received on Thu Jul 21 2016 - 05:00:02 PDT
