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.
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>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Fri Nov 03 2017 - 18:00:03 PDT
