Hi, Akshay
If you applied all the updates in Amber16, the &pmd should work.
I checked your mdin files and in cv.in cv_ni should be 129 because the
number zero also counts.
Also I strongly recommend you to update to Amber18 to use since there are
several updates and bug fix.
If you still encounter some error, you can send me the mdin files, I can
have a try.
Best
Feng
On Sun, May 5, 2019 at 11:30 AM Akshay Prabhakant <
akshayresearch16.gmail.com> wrote:
> Hello to the AMBER Community,
>
> I need help debugging my input files for an umbrella sampling simulation on
> a simple protein system using the 'pmemd' binary in Amber16.
>
> I have already performed minimization, equilibration and production runs on
> it. I plan to use the post-equilibriation run structure for umbrella
> sampling. I am using AMBER/16 currently, and CANNOT MAKE A SHIFT TO ANY
> OTHER VERSION.
>
> My collective variable is the distance of centre of masses of two groups of
> atoms. I plan on including another collective variable, which happens to be
> the angle between centre of masses of 3 groups of atoms.
>
> It is my humble request to be provided with a working piece of code(mdin
> and collective variable file), in AMBER/2016, in "pmemd", which takes care
> of both the collective variables(distance between COMs of two given groups
> of atoms, angle between COMs of 3 given groups of atoms) being
> harmonically restrained about a given value.
>
> Thanks in advance.
>
> I have tried to go through some methods which I could find, for instance
> the :
>
> 1. nfe method, using the &colvar(in collective variable file),
> &pmd(namelist in mdin file), but could not manage to write a working piece
> of code, for my mdin and collective variable input files.
>
> mdin code:
> &cntrl
> imin=0, ! normal MD run
> irest=1, ntx=5, ! we are generating random initial velocities
> from a boltzmann distribution and only read in the coordinates from the
> inpcrd
> ntb=2, !
> ntp=1, tautp=1.0, ! constant pressure periodic boundaries
> cut=10.0 ! cutoff
> ntc=2, ntf=2, ! SHAKE should be turned on and used to
> constrain bonds involving hydrogen
> tempi=300.0, temp0=300.0, ! equilibriate at 300K
> ntt=3, gamma_ln=1.0, ! the langevin dynamics should be used to
> control the temperature using a collision frequency of 1.0 ps-1
> ig=-1, ! change the random seed (ig) between restarts
> nstlim=500, dt=0.002, ! total simulation time of 1 ps
> ntpr=25, ntwx=50, ! write to the output file (ntpr) every 0.05 ps, to
> the trajectory file (ntwx) every 0.1 ps
> ntwr=50, ! write a restart file (ntwr) every 0.1 ps,
> ioutfm=1,
> nmropt=1, ! NMR restraints and weight changes will be
> read.
> infe=1,
> /
> &pmd
> output_freq=50
> output_file='pmd.txt'
> cv_file = ’cv.in’
> /
>
>
> cv.in:
> &colvar
> cv_type = 'COM_DISTANCE'
> cv_ni = 128
> cv_i = 2845, 2846, 2847, 2848, 2849, 2850, 2851, 2852, 2853, 2854, 2855,
> 2856, 2857, 2858, 2859, 2860, 2861, 2862, 2863, 2864, 2865, 2866, 2867,
> 2868, 2869, 2870, 2871, 2872, 2873, 2874, 2875, 2876, 2877, 2878, 2879,
> 2880, 2881, 2882, 2883, 2884, 2885, 2886, 2887, 2888, 2889, 2890, 2891,
> 2892, 2893, 2894, 2895, 2896, 2897, 2898, 2899, 2900, 2901, 2902, 2903,
> 2904, 2905, 2906, 2907, 2908,0, 6191, 6192, 6193, 6194, 6195, 6196, 6197,
> 6198, 6199, 6200, 6201, 6202, 6203, 6204, 6205, 6206, 6207, 6208, 6209,
> 6210, 6211, 6212, 6213, 6214, 6215, 6216, 6217, 6218, 6219, 6220, 6221,
> 6222, 6223, 6224, 6225, 6226, 6227, 6228, 6229, 6230, 6231, 6232, 6233,
> 6234, 6235, 6236, 6237, 6238, 6239, 6240, 6241, 6242, 6243, 6244, 6245,
> 6246, 6247, 6248, 6249, 6250, 6251, 6252, 6253, 6254,
> anchor_position = 17.43
> anchor_strength = 10000
> /
>
> Error encountered: Cannot read &pmd and &colvar namelists.
>
> 2. Using the ncsu_pmd section in the mdin file itself. but both sander and
> pmemd could neither read the restraints nor the values of collective
> variables, mentioned in the section.
>
> mdin file:
> &cntrl
> imin=0, ! normal MD run
> irest=1, ntx=5, ! we are generating random initial velocities
> from a boltzmann distribution and only read in the coordinates from the
> inpcrd
> ntb=2, !
> ntp=1, tautp=1.0, ! constant pressure periodic boundaries
> cut=10.0 ! cutoff
> ntc=2, ntf=2, ! SHAKE should be turned on and used to
> constrain bonds involving hydrogen
> tempi=300.0, temp0=300.0, ! equilibriate at 300K
> ntt=3, gamma_ln=1.0, ! the langevin dynamics should be used to
> control the temperature using a collision frequency of 1.0 ps-1
> ig=-1, ! change the random seed (ig) between restarts
> nstlim=500, dt=0.002, ! total simulation time of 1 ps
> ntpr=25, ntwx=50, ! write to the output file (ntpr) every 0.05 ps, to
> the trajectory file (ntwx) every 0.1 ps
> ntwr=50, ! write a restart file (ntwr) every 0.1 ps,
> ioutfm=1,
> nmropt=1, ! NMR restraints and weight changes will be
> read.
> /
> ncsu_pmd
> output_file = ’pmd.txt’
> output_freq = 50
> variable ! first
> type = DISTANCE
> i = (2847,6193)
> anchor_position = 14.74
> anchor_strength = 500.0
> end variable
> end ncsu_pmd
>
> Error encountered: rfree: Error decoding variable 1 3 from
>
> 3. Usage of &wt namelist(in mdin file) and &rst(in collective variable
> file), here too pmemd and sander were unable to read the variable and
> restraint values. reference
> <http://ambermd.org/tutorials/advanced/tutorial17/section2.htm> for this
> method.
>
> mdin file:
> &cntrl
> imin=0, ! normal MD run
> irest=1, ntx=5, ! we are generating random initial velocities
> from a boltzmann distribution and only read in the coordinates from the
> inpcrd
> ntb=2, !
> ntp=1, tautp=1.0, ! constant pressure periodic boundaries
> cut=10.0 ! cutoff
> ntc=2, ntf=2, ! SHAKE should be turned on and used to
> constrain bonds involving hydrogen
> tempi=300.0, temp0=300.0, ! equilibriate at 300K
> ntt=3, gamma_ln=1.0, ! the langevin dynamics should be used to
> control the temperature using a collision frequency of 1.0 ps-1
> ig=-1, ! change the random seed (ig) between restarts
> nstlim=500, dt=0.002, ! total simulation time of 1 ps
> ntpr=25, ntwx=50, ! write to the output file (ntpr) every 0.05 ps, to
> the trajectory file (ntwx) every 0.1 ps
> ntwr=50, ! write a restart file (ntwr) every 0.1 ps,
> ioutfm=1,
> nmropt=1, ! NMR restraints and weight changes will be
> read.
> /
> &wt
> type='END'
> &end
> DISANG=cv.in
>
> cv.in:
>
> Restraints for bonds
> &rst
> iat=-1,-1,
> igr1=2845, 2846, 2847, 2848, 2849, 2850, 2851, 2852, 2853, 2854, 2855,
> 2856, 2857, 2858, 2859, 2860, 2861, 2862, 2863, 2864, 2865, 2866, 2867,
> 2868, 2869, 2870, 2871, 2872, 2873, 2874, 2875, 2876, 2877, 2878, 2879,
> 2880, 2881, 2882, 2883, 2884, 2885, 2886, 2887, 2888, 2889, 2890, 2891,
> 2892, 2893, 2894, 2895, 2896, 2897, 2898, 2899, 2900, 2901, 2902, 2903,
> 2904, 2905, 2906, 2907, 2908,
> igr2= 6191, 6192, 6193, 6194, 6195, 6196, 6197, 6198, 6199, 6200, 6201,
> 6202, 6203, 6204, 6205, 6206, 6207, 6208, 6209, 6210, 6211, 6212, 6213,
> 6214, 6215, 6216, 6217, 6218, 6219, 6220, 6221, 6222, 6223, 6224, 6225,
> 6226, 6227, 6228, 6229, 6230, 6231, 6232, 6233, 6234, 6235, 6236, 6237,
> 6238, 6239, 6240, 6241, 6242, 6243, 6244, 6245, 6246, 6247, 6248, 6249,
> 6250, 6251, 6252, 6253, 6254,
> r1=-999, r2=17.43,r3=17.43,r4=999,
> rk2=500.0, rk3=500.0
> /
>
> Error encountered: rfree: Error decoding variable 1 3 from
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>
--
Feng Pan
PostDoc
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Tue May 07 2019 - 09:30:02 PDT
