Hi Justin,
Thank you so much for your reply. Please find attached some of the input
files for the dye molecule. The table file contains the user defined
dihedral potential and the negative of its first derivative from -180 to
180 degrees. The "k" multiplier of the spline is 1 in this case. Looking
forward to your suggestions..
Thanks,
Durba
Date: Tue, 11 May 2010 18:37:41 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] energy_increase_NVE_run
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Durba Roy wrote:
> Hi Gromacs Users,
> > I am trying to run a NVE simulation of a single dye molecule
jumping > from state S0 to state S1. I have starting coordinates and
velocities > from a previous NPT run of the same system at S0,
however, the charges > are new, that of S1. I didnot generate any
Maxwell-velocity for the NVE > run and followed the instructions that
rlist should be ~0.3 nm larger > than rcoulomb and rvdw. I also
increased Lincs_iteration value and the > table extension. Please
note that I am using a tabulated interaction > potential for a
particular dihedral.
>
Simulating under a different ensemble, then changing simulation
parameters (like cutoffs) does not bode well for simulation stability.
Note, too, that there are other factors that can influence the stability
of an NVE run:
http://www.gromacs.org/Documentation/Terminology/NVE
> The problem is, an increasing total energy during the NVE run and
the > molecule collapses followed by segmentation fault. However, the
S0-S1 > jump sim runs fine in NPT ensemble.
> > Also, when I use null potential for the dihedral the NVE job runs
fine.
> Kind of confused and will really appreciate your help.
>
If your system is stable without the tabulated potential, then breaks
down when you use it, it seems pretty clear that however you're treating
this dihedral is causing your simulation to break. Without more
specific details (your full .mdp file, the parameters you're using for
the dihedral, etc), it will be hard to give you any further help.
-Justin
> Thanks,
> Durba
#include "ffoplsaa.itp"
#include "dmn.itp"
[ moleculetype ]
; Name nrexcl
dmn 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_145 1 DMN CA 1 -0.245095 12.011
2 opls_145 1 DMN CA 2 -0.223432 12.011
3 opls_145 1 DMN CA 3 0.463682 12.011
4 opls_145 1 DMN CA 4 -0.378623 12.011
5 opls_145 1 DMN CA 5 -0.111455 12.011
6 opls_145 1 DMN CA 6 0.112231 12.011
7 opls_146 1 DMN HA 7 0.172026 1.008
8 opls_146 1 DMN HA 8 0.185272 1.008
9 opls_146 1 DMN HA 9 0.175581 1.008
10 opls_146 1 DMN HA 10 0.149556 1.008
11 opls_902 1 DMN NT 11 0.202322 14.007
12 opls_918 1 DMN CT 12 -0.334965 12.011
13 opls_911 1 DMN HC 13 0.133420 1.008
14 opls_911 1 DMN HC 14 0.146276 1.008
15 opls_911 1 DMN HC 15 0.133321 1.008
16 opls_918 1 DMN CT 16 -0.334880 12.011
17 opls_911 1 DMN HC 17 0.150698 1.008
18 opls_911 1 DMN HC 18 0.126718 1.008
19 opls_911 1 DMN HC 19 0.126555 1.008
20 opls_142 1 DMN CM 20 -0.327443 12.011
21 opls_144 1 DMN HA 21 0.158950 1.008
22 opls_141 1 DMN CM 22 -0.489620 12.011
23 opls_754 1 DMN CZ 23 0.564012 12.011
24 opls_754 1 DMN CZ 24 0.564012 12.011
25 opls_753 1 DMN NZ 25 -0.559559 14.007
26 opls_753 1 DMN NZ 26 -0.559559 14.007
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 6 1
1 7 1
2 3 1
2 8 1
3 4 1
3 20 1
4 5 1
4 9 1
5 6 1
5 10 1
6 11 1
11 12 1
11 16 1
12 13 1 0.096069 284702.4
12 14 1 0.095957 284702.4
12 15 1 0.095963 284702.4
16 17 1 0.095948 284702.4
16 18 1 0.096035 284702.4
16 19 1 0.095931 284702.4
20 21 1
20 22 1
22 23 1 0.143197 322383.6
22 24 1 0.142943 322383.6
23 26 1
24 25 1
[ pairs ]
; ai aj ak funct
1 4 1
1 10 1
1 12 1
1 16 1
1 20 1
2 5 1
2 9 1
2 11 1
2 21 1
2 22 1
3 6 1
3 7 1
3 10 1
3 23 1
3 24 1
4 8 1
4 11 1
4 21 1
4 22 1
5 7 1
5 12 1
5 16 1
5 20 1
6 8 1
6 9 1
6 13 1
6 14 1
6 15 1
6 17 1
6 18 1
6 19 1
7 8 1
7 11 1
8 20 1
9 10 1
9 20 1
10 11 1
20 25 1
20 26 1
21 23 1
21 24 1
23 25 1
24 26 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1
1 2 8 1
1 6 5 1
1 6 11 1
2 1 6 1
2 1 7 1
2 3 4 1
2 3 20 1
3 2 8 1
3 4 5 1
3 4 9 1
3 20 21 1
3 20 22 1 131.60705 700
4 3 20 1
4 5 6 1
4 5 10 1
5 4 9 1
5 6 11 1
6 1 7 1
6 5 10 1
6 11 12 1
6 11 16 1
11 12 13 1 109.50892 293.0760
11 12 14 1 109.43765 293.0760
11 12 15 1 109.42332 293.0760
11 16 17 1 109.46511 293.0760
11 16 18 1 109.47571 293.0760
11 16 19 1 109.48231 293.0760
12 11 16 1
13 12 14 1 109.51755 276.3288
14 12 15 1 109.38895 276.3288
13 12 15 1 109.55090 276.3288
17 16 18 1 109.46092 276.3288
18 16 19 1 109.46239 276.3288
17 16 19 1 109.48088 276.3288
20 22 23 1 119.30515 586.1520
20 22 24 1 125.76458 586.1520
21 20 22 1
22 23 26 1 179.35512 1256.0400
22 24 25 1 178.22837 1256.0400
23 22 24 1 114.89824 586.1520
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3
1 2 3 4 3
1 2 3 20 3
1 6 5 4 3
1 6 5 10 3
1 6 11 12 3 5.1875 35.9563 -14.3649 -26.7788 0.
0.
1 6 11 16 3 5.1875 35.9563 -14.3649 -26.7788 0.
0.
2 1 6 5 3
2 1 6 11 3
2 3 4 5 3
2 3 4 9 3
2 3 20 21 3 -1.79284 -0.42886 2.22170 0.00000 0.00000
0.00000
2 3 20 22 3
3 2 1 6 3
3 2 1 7 3
3 4 5 6 3
3 4 5 10 3
3 20 22 23 8 0 1
3 20 22 24 8 0 1
4 3 2 8 3
4 3 20 21 3 -1.79284 -0.42886 2.22170 0.00000 0.00000
0.00000
4 3 20 22 3
4 5 6 11 3
5 4 3 20 3
5 6 1 7 3
5 6 11 12 3 5.1875 35.9563 -14.3649 -26.7788 0. 0.
5 6 11 16 3 5.1875 35.9563 -14.3649 -26.7788 0. 0.
6 1 2 8 3
6 5 4 9 3
6 11 12 13 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
6 11 12 14 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
6 11 12 15 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
6 11 16 17 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
6 11 16 18 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
6 11 16 19 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
7 1 2 8 3
7 1 6 11 3
8 2 3 20 3
9 4 3 20 3
9 4 5 10 3
10 5 6 11 3
12 11 16 17 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
12 11 16 18 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
12 11 16 19 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
16 11 12 13 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
16 11 12 14 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
16 11 12 15 3 1.1723 3.5169 0.0000 -4.6892 0. 0.
[ dihedrals]
; aj ak ai al funct
22 20 23 24 2 0.000000 7000.40000
20 3 21 22 2 0.000000 7000.40000
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
2 3 20 22 1 1 0 0 1 2
2 3 20 21 1 1 180 0 1 2
8 2 3 20 1 1 0 0 1 2
1 6 11 16 1 1 180 0 1 2
1 6 11 12 1 1 0 0 1 2
[ system ]
DMN
[ molecules ]
dmn 1
e
; File 'mdout.mdp' was generated
; By user: spoel (291)
; On host: chagall
; At date: Mon Dec 15 13:52:23 2003
;
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.0001
nsteps = 100000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm =
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-temp =
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol =
emstep = 0.001
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0.001
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 10
nstvout = 10
nstfout = 10
; Checkpointing helps you continue after crashes
nstcheckpoint = 10
; Output frequency for energies to log file and energy file
nstlog = 50
nstenergy = 50
; Output frequency and precision for xtc file
nstxtcout = 1000
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps = bz-dmn mal-dmn
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.2
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME-switch
rcoulomb-switch = 0.8
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Shift
; cut-off lengths
rvdw-switch = 0.8
rvdw = 1.1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx =
fourier_ny =
fourier_nz =
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = no
; Groups to couple separately
tc-grps = system
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility =4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 300
gen_seed = 1993
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 2
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl = bz-dmn mal-dmn
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = yes
dihre-fc = 1000
dihre-tau = 0
; Output frequency for dihedral values to energy file
nstdihreout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =frz
freezedim =N N N
cos-acceleration = 0
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
Generated by trjconv : DMN t= 0.01000
26
1DMN CA 1 0.719 0.810 2.565 0.1493 0.3201 0.3272
1DMN CA 2 0.697 0.948 2.566 -0.1723 0.2696 0.2397
1DMN CA 3 0.574 1.001 2.524 -0.2205 0.1112 0.1788
1DMN CA 4 0.477 0.909 2.484 0.2199 -0.0668 -0.4691
1DMN CA 5 0.499 0.770 2.484 0.1848 -0.0723 -0.4693
1DMN CA 6 0.620 0.717 2.530 0.0458 0.3903 0.4337
1DMN HA 7 0.816 0.785 2.605 -0.4928 -2.4933 0.2333
1DMN HA 8 0.777 1.016 2.592 0.1983 0.0095 -0.2153
1DMN HA 9 0.380 0.935 2.446 0.8270 2.3154 -0.4874
1DMN HA 10 0.417 0.709 2.449 -0.2049 0.7998 -1.1274
1DMN NT 11 0.646 0.586 2.533 0.2074 0.4144 0.0883
1DMN CT 12 0.765 0.533 2.565 -0.2513 -0.6967 -0.0348
1DMN HC 13 0.777 0.557 2.657 -1.2795 2.2818 -0.6167
1DMN HC 14 0.762 0.437 2.558 -1.2563 -0.5287 -2.8258
1DMN HC 15 0.827 0.571 2.502 -1.4140 0.4923 -0.4742
1DMN CT 16 0.554 0.495 2.498 0.6720 -0.1746 0.4017
1DMN HC 17 0.589 0.406 2.506 0.2739 -0.3767 -0.1087
1DMN HC 18 0.481 0.512 2.558 1.8149 -0.2413 1.8349
1DMN HC 19 0.535 0.520 2.408 3.0121 -0.8980 -0.3185
1DMN CM 20 0.536 1.139 2.517 -0.1618 0.1030 -0.2868
1DMN HA 21 0.436 1.167 2.487 -0.2545 -0.1826 -0.2403
1DMN CM 22 0.608 1.249 2.545 -0.1505 0.0220 0.0092
1DMN CZ 23 0.546 1.378 2.532 -0.1566 0.0156 -0.0198
1DMN CZ 24 0.745 1.244 2.585 -0.0720 -0.0219 -0.2633
1DMN NZ 25 0.852 1.232 2.627 -0.2488 -0.7116 0.0036
1DMN NZ 26 0.509 1.488 2.524 -0.1210 0.0412 0.1804
2.94560 2.94560 2.94560
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