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
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>
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Received on Mon Nov 27 2017 - 16:30:03 PST
