I changed the cutoff to 1000 and that works.
Thank you!
Best wishes
Yuan Min
> -----原始邮件-----
> 发件人: "Hai Nguyen" <nhai.qn.gmail.com>
> 发送时间: 2017-11-28 08:27:48 (星期二)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] STOP PMEMD Terminated Abnormally
>
> Yes, just follow the error message.
> Hai
>
> On Mon, Nov 27, 2017 at 7:17 PM MinYuan <minyuan.mail.ustc.edu.cn> wrote:
>
> > the out file as follows:
> > -----------------------
> >
> > -------------------------------------------------------
> > Amber 16 PMEMD 2016
> > -------------------------------------------------------
> >
> > | PMEMD implementation of SANDER, Release 16
> >
> > | Run on 11/28/2017 at 08:13:50
> >
> > | Executable path: pmemd.cuda
> > | Working directory: /home/miny/amber/project/tutorials/18CpH
> > | Hostname: Unknown
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: heat.mdin
> > | MDOUT: 4LYT.heat.mdout
> > | INPCRD: 4LYT.min.rst7
> > | PARM: 4LYT.parm7
> > | RESTRT: 4LYT.heat.rst7
> > | REFC: 4LYT.min.rst7
> > | MDVEL: mdvel
> > | MDEN: mden
> > | MDCRD: 4LYT.heat.nc
> > | MDINFO: mdinfo
> > | MDFRC: mdfrc
> >
> >
> > Here is the input file:
> >
> > Implicit solvent constant pH initial heating mdin
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > ntpr=500, ntwx=500, nstlim=1000000,
> > dt=0.002, ntt=3, tempi=100,
> > temp0=300, tautp=2.0, ig=-1,
> > ntp=0, ntc=2, ntf=2, cut=30,
> > ntb=0, igb=2, tol=0.000001,
> > nrespa=1, saltcon=0.1, icnstph=1,
> > solvph=7.5, ntcnstph=100000000,
> > gamma_ln=5.0, ntwr=500, ioutfm=1,
> > nmropt=1, ntr=1, restraint_wt=2.0,
> > restraintmask='.CA,C,O,N',
> > /
> > &wt
> > TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
> > VALUE1=10.0, VALUE2=300.0,
> > /
> > &wt TYPE='END' /
> >
> >
> > Note: ig = -1. Setting random seed to 802334 based on wallclock time in
> > microseconds.
> > CUDA (GPU): Implementation does not support the use of a cutoff in GB
> > simulations.
> > Require cut > 999.0d0.
> >
> > Input errors occurred. Terminating execution.
> > --------------------------------------------------
> >
> > Is it the matter of the cutoff in GB simulations??
> >
> > Best wishes
> > Yuan Min
> >
> > > -----原始邮件-----
> > > 发件人: "Elvis Martis" <elvis.martis.bcp.edu.in>
> > > 发送时间: 2017-11-28 00:10:36 (星期二)
> > > 收件人: "AMBER Mailing List" <amber.ambermd.org>
> > > 抄送:
> > > 主题: Re: [AMBER] STOP PMEMD Terminated Abnormally
> > >
> > > Hi,
> > > Can you post the out file?
> > >
> > > Best Regards
> > > Elvis Martis
> > > Mumbai, INDIA.
> > >
> > > ________________________________________
> > > From: MinYuan <minyuan.mail.ustc.edu.cn>
> > > Sent: 27 November 2017 21:38
> > > To: amber.ambermd.org
> > > Subject: [AMBER] STOP PMEMD Terminated Abnormally
> > >
> > > Hi,
> > >
> > > I learned tutorial at
> > http://ambermd.org/tutorials/advanced/tutorial18/section2.htm
> > > instead of using command "mpiexec -n 4 sander.MPI -i heat.mdin -c
> > 4LYT.min.rst7 -p 4LYT.parm7 -ref 4LYT.min.rst7 -cpin 4LYT.cpin -o
> > 4LYT.heat.mdout -r 4LYT.heat.rst7 -x 4LYT.heat.nc"
> > > I used command "pmemd.cuda -O -i heat.mdin -c 4LYT.min.rst7 -p
> > 4LYT.parm7 -ref 4LYT.min.rst7 -cpin 4LYT.cpin -o 4LYT.heat.mdout -r
> > 4LYT.heat.rst7 -x 4LYT.heat.nc"
> > >
> > > and error comes as:STOP PMEMD Terminated Abnormally!
> > >
> > > Looking forward to hear your reply soon.
> > >
> > > Best wishes
> > >
> > > Yuan Min
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Nov 27 2017 - 17:00:02 PST
