Thanks for your reply. But can not understand COM_DISTANCE reaction coordinate will work in Amber14 or not, because in the amber14 manual this reaction coordinate is not mentioned but in amber16 and amber17 manual it is mentioned. I include the CV definition directly in the mdin file as ncsu_pmd and it is running in amber14, but I can not understand COM_DISTANCE reaction coordinate is working or not. During run it is not printing output pmd.txt file. My modified input file are given below
NVT production for 12.8 Ang
&cntrl
ntx = 1, irest = 0,
nstlim = 5000, dt = 0.002,
irest=0, ntt=3, gamma_ln=5.0,
temp0 = 300.0,
ntc=2, ntf=2, nscm=1000,
ntb=1, ntp=0
cut=10.0,
ntpr = 500, ntwr = 1000, ntwx = 1000,
nmropt=1,
numexchg=500,
/
ncsu_pmd
output_file = 'pmd.txt’
output_freq = 50
variable
type = COM_DISTANCE
i = (168,169,171,173,174,177,178,179,231,232,234,236,237,240,241,242,514,515,517,518,519,520,521,523,524,527,528,577,578,580,581,582,583,584,586,587,590,591,0,547,548,550,552,553,556,557,558,0)
anchor_position = 12.8
anchor_strength = 10.0
end variable
end ncsu_pmd
&wt
type='END',
&end
> -----Original Messages-----
> From: "Feng Pan" <fpan3.ncsu.edu>
> Sent Time: 2017-11-04 08:47:37 (Saturday)
> To: "AMBER Mailing List" <amber.ambermd.org>
> Cc:
> Subject: Re: [AMBER] H-REMD
>
> Hi,
>
> The Amber14 still uses the old style of input, so you should
> include the CV definition directly in the mdin file as
> ncsu_pmd
> ...
> variable
> ...
> end variable
> end ncsu_pmd
>
>
> You can check the amber14 manual for examples
>
> Feng
>
> On Fri, Nov 3, 2017 at 6:53 AM, Dr. MANAS MONDAL <manas.pku.edu.cn> wrote:
>
> > Hi,
> > I am trying to do umbrella sampling with REMD. Is COM_DISTANCE reaction
> > coordinates will work in AMBER14 ?
> > I want to use the following input file HREMD simulation:
> >
> > NVT production for 4.8 Ang
> > &cntrl
> > ntx = 1, irest = 0,
> > nstlim = 5000, dt = 0.002,
> > irest=0, ntt=3, gamma_ln=5.0,
> > temp0 = 300.0,
> > ntc=2, ntf=2, nscm=1000,
> > ntb=1, ntp=0
> > cut=10.0,
> > ntpr = 500, ntwr = 1000, ntwx = 1000,
> > numexchg=500,
> > /
> >
> > ncsu_pmd
> > output_file = 'pmd_12.txt'
> > output_freq = 50
> > cv_file = 'cv_12.in'
> > end ncsu_pmd
> > /
> > &wt
> > type='END',
> > &end
> >
> >
> > cv file
> > &colvar
> > cv_type = 'COM_DISTANCE'
> > cv_i = 168,169,171,173,174,177,178,179,231,232,234,236,237,240,
> > 241,242,514,515,517,518,519,520,521,523,524,527,528,577,
> > 578,580,581,582,583,584,586,587,590,591,0,547,548,550,552,
> > 553,556,557,558,0
> > anchor_position = 0.4
> > anchor_strength = 10.0
> > /
> >
> > Please suggest.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
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> AMBER.ambermd.org
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Received on Fri Nov 03 2017 - 20:30:03 PDT
