Does your amber installation pass all of the tests?
On Jul 21, 2016 10:43 AM, "乔艳" <yanqiao.zzu.edu.cn> wrote:
> 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.
>
> ----- 原始邮件 -----
> 发件人: Carlos Simmerling <carlos.simmerling.gmail.com>
> 收件人: AMBER Mailing List <amber.ambermd.org>
> 已发送邮件: Thu, 21 Jul 2016 19:54:41 +0800 (CST)
> 主题: 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, 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
> >
> >
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> >
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Received on Thu Jul 21 2016 - 08:00:03 PDT
