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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Received on Sun May 05 2019 - 09:00:02 PDT
