[AMBER] ظ Re: MD simulation can not proceed normally

From: <yanqiao.zzu.edu.cn>
Date: Thu, 21 Jul 2016 22:28:13 +0800 (CST)

For the single processor, it seems ok. It is very strange since the parallel mode is normal in the minimization steps and in other systems that I tried. I feel puzzled.

----- ԭʼʼ -----
: Carlos Simmerling <carlos.simmerling.gmail.com>
ռ: AMBER Mailing List <amber.ambermd.org>
ѷʼ: Thu, 21 Jul 2016 19:54:41 +0800 (CST)
: Re: [AMBER] MD simulation can not proceed normally

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, <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
>
>
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Received on Thu Jul 21 2016 - 08:00:02 PDT
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