The COM_DISTANCE should work in Amber14 although it is not included in the
manual, are you running using Sander
or pmemd? And since you are running HREMD, are you running with replicas? I
saw you have numexchg defined, make
sure you have the correct groupfile for HREMD.
And you can send me your mdout file to check whether pmd is read,
and you needn't to add &wt and set nmropt=1 in your mdin since I ddin't see
any NMR restraint
Best
Feng
On Fri, Nov 3, 2017 at 11:29 PM, Dr. MANAS MONDAL <manas.pku.edu.cn> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 03 2017 - 21:00:03 PDT
