hi gmx-users
sorry for this pack of emails. the page has not a good format. you can find my
text included to this email.
thanks
hi gmx-users
In order to discover the miscalculation that gromacs computes in a system of
450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one
molecule in vacuum just to calculate by hand all the energies. the mdp file
that i use is
; 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 = 0.001
nsteps = 500000
; 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 = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp = 300
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; 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 = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 50
nstenergy = 50
; Output frequency and precision for xtc file
nstxtcout = 100
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 =
; 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 = 1.5
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.5
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.5
; 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 = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; 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 = nose-hoover
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 298
; Pressure coupling
Pcoupl = Berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1
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 = yes
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 = 1
; 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 =
the top file is
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 0 0.5
[ atomtypes ]
; type mass charge ptype c6 c12
CH3 15.035 0.000 A 9.0638e-3 2.5206e-5
CH2 14.027 0.000 A 5.8108e-3 2.2071e-5
OS 15.999 0.000 A 8.8147e-4 4.2477e-7
OA 15.999 0.000 A 2.3465e-3 1.7802e-6
HO 1.008 0.000 A 0.0000e00 0.0000e00
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 0.000 15.035
2 CH2 1 DRG CAC 1 0.000 14.027
3 CH2 1 DRG CAE 1 0.000 14.027
4 CH2 1 DRG CAF 1 0.000 14.027
5 CH2 1 DRG CAG 2 0.000 14.027
6 CH2 1 DRG CAI 2 0.250 14.027
7 OS 1 DRG OAM 2 -0.500 15.999
8 CH2 1 DRG CAK 2 0.250 14.027
9 CH2 1 DRG CAJ 3 0.250 14.027
10 OS 1 DRG OAL 3 -0.500 15.999
11 CH2 1 DRG CAH 3 0.250 14.027
12 CH2 1 DRG CAD 4 0.265 14.027
13 OA 1 DRG OAB 4 -0.700 15.999
14 HO 1 DRG HAA 4 0.435 1.008
[ bonds ]
; ai aj funct c0 c1
1 2 1 0.15400 517488.48
2 3 1 0.15400 517488.48
3 4 1 0.15400 517488.48
4 5 1 0.15400 517488.48
5 6 1 0.15400 517488.48
6 7 1 0.14100 618809.04
7 8 1 0.14100 618809.04
8 9 1 0.15400 517488.48
9 10 1 0.14100 618809.04
10 11 1 0.14100 618809.04
11 12 1 0.15400 517488.48
12 13 1 0.14300 618809.04
13 14 1 0.09450 618809.04
[ angles ]
; ai aj ak funct c0 c1
1 2 3 1 114.00 519.65
2 3 4 1 114.00 519.65
3 4 5 1 114.00 519.65
4 5 6 1 114.00 519.65
5 6 7 1 112.00 418.22
6 7 8 1 112.00 502.19
7 8 9 1 112.00 418.22
8 9 10 1 112.00 418.22
9 10 11 1 112.00 502.19
10 11 12 1 112.00 418.22
11 12 13 1 109.47 419.05
12 13 14 1 108.50 460.62
[ pairs ]
; ai aj funct
1 4 1 0 0 0 0
2 5 1 0 0 0 0
3 6 1 0 0 0 0
4 7 1 0 0 0 0
5 8 1 0 0 0 0
6 9 1 0 0 0 0
7 10 1 0 0 0 0
8 11 1 0 0 0 0
9 12 1 0 0 0 0
10 13 1 0 0 0 0
11 14 1 0 0 0 0
;
10 14 2 0 0 0 0 3.325789e-7
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4
c5
1 2 3 4 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00
0.000000e+00
2 3 4 5 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00
0.000000e+00
3 4 5 6 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00
0.000000e+00
4 5 6 7 3 6.983076 17.736182 0.886988 -25.606246 0.000000e+00
0.000000e+00
5 6 7 8 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00
0.000000e+00
6 7 8 9 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00
0.000000e+00
7 8 9 10 3 8.368267 25.104800 4.184175 -33.473067 0.000000e+00
0.000000e+00
8 9 10 11 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00
0.000000e+00
9 10 11 12 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00
0.000000e+00
10 11 12 13 3 8.368267 25.104800 4.184175 -33.473067 0.000000e+00
0.000000e+00
11 12 13 14 3 2.822015 2.943074 0.485066 -6.250155 0.000000e+00
0.000000e+00
[ system ]
ciej
[ molecules ]
DRG 1
and the gro file is
PRODRG COORDS
14
1DRG CAA 1 0.313 0.879 0.001
1DRG CAC 2 0.381 0.742 0.002
1DRG CAE 3 0.534 0.757 0.000
1DRG CAF 4 0.601 0.620 0.001
1DRG CAG 5 0.754 0.634 -0.001
1DRG CAI 6 0.821 0.497 0.001
1DRG OAM 7 0.964 0.513 -0.001
1DRG CAK 8 1.026 0.383 0.001
1DRG CAJ 9 1.177 0.399 -0.001
1DRG OAL 10 1.238 0.268 0.001
1DRG CAH 11 1.382 0.282 0.000
1DRG CAD 12 1.446 0.143 0.002
1DRG OAB 13 1.588 0.156 0.001
1DRG HAA 14 1.630 0.066 0.002
4.00000 4.00000 4.00000
as you can see at top file there is a line in pairs which syntaxis is
10 14 2 0 0 0 0 3.325789e-7
it is an extra interaction that must be applied to the molecule according to
the formula 3.325789e-7/r^12 the only way i could think importing this
interaction as i have mentioned several times was the above.
i did three simulations
1) leaving the top file as it is above
2) deleting the [pairs] and all the lines below
3) deleting only the last line of the [pairs]
the results with usage of the command gmxdump -s topol.tpr | less
for step 0 are below
1)leaving the top file as it is above
I)from md.log
Step Time Lambda
0 0.00000 0.00000
Grid: 3 x 3 x 3 cells
Long Range LJ corr.: <C6> 3.8522e-03
Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091
Energies (kJ/mol)
Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)
5.70628e+00 8.37083e+00 6.80805e-03 1.72679e+02 -3.25801e+00
Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En.
-7.32091e-03 -2.93587e+01 -1.21273e+02 3.28661e+01 3.94838e+01
Total Energy Temperature Pressure (bar) Cons. rmsd ()
7.23499e+01 3.65291e+02 4.25495e+01 3.43881e-07
II) from gmxdump
ffparams:
atnr=5
ntypes=41
functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05
functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05
functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07
functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06
functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[20]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB=
1.14000e+02, ctB= 5.19650e+02
functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB=
1.12000e+02, ctB= 4.18220e+02
functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB=
1.12000e+02, ctB= 5.02190e+02
functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB=
1.09470e+02, ctB= 4.19050e+02
functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB=
1.08500e+02, ctB= 4.60620e+02
functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01,
rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00,
rbcB[3]=-2.63176327e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01,
rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01,
rbcB[3]=-2.56062469e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00,
rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00,
rbcB[3]=-1.85645523e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01,
rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00,
rbcB[3]=-3.34730682e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00,
rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01,
rbcB[3]=-6.25015497e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[35]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B=
0.00000000e+00, c12B= 0.00000000e+00
functype[36]=LJC14_Q, fqq= 0.00000000e+00, qi= 0.00000000e+00, qj=
0.00000000e+00, c6= 0.00000000e+00, c12= 3.32578907e-07
functype[37]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01
functype[38]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02
functype[39]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01
functype[40]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01
fudgeQQ = 0.5
2) deleting the [pairs] and all the lines below
I)from md.log
Step Time Lambda
0 0.00000 0.00000
Grid: 3 x 3 x 3 cells
Long Range LJ corr.: <C6> 3.8522e-03
Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091
Energies (kJ/mol)
Angle Ryckaert-Bell. LJ (SR) Disper. corr. Coulomb (SR)
5.70628e+00 8.37083e+00 -3.25801e+00 -7.32091e-03 -2.93587e+01
Coul. recip. Potential Kinetic En. Total Energy Temperature
-1.21273e+02 -1.39819e+02 3.94033e+01 -1.00416e+02 3.64546e+02
Pressure (bar) Cons. rmsd ()
3.09781e+01 3.89303e-07
II) from gmxdump
ffparams:
atnr=5
ntypes=39
functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05
functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05
functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07
functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06
functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[20]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB=
5.19650e+02
functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB=
1.12000e+02, ctB= 4.18220e+02
functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB=
1.12000e+02, ctB= 5.02190e+02
functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB=
1.09470e+02, ctB= 4.19050e+02
functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB=
1.08500e+02, ctB= 4.60620e+02
functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01,
rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00,
rbcB[3]=-2.63176327e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01,
rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01,
rbcB[3]=-2.56062469e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00,
rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00,
rbcB[3]=-1.85645523e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01,
rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00,
rbcB[3]=-3.34730682e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00,
rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01,
rbcB[3]=-6.25015497e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[35]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01
functype[36]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02
functype[37]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01
functype[38]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01
fudgeQQ = 0.5
3) deleting only the last line of the [pairs]
I)from md.log
Step Time Lambda
0 0.00000 0.00000
Grid: 3 x 3 x 3 cells
Long Range LJ corr.: <C6> 3.8522e-03
Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091
Energies (kJ/mol)
Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)
5.70628e+00 8.37083e+00 0.00000e+00 1.72679e+02 -3.25801e+00
Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En.
-7.32091e-03 -2.93587e+01 -1.21273e+02 3.28593e+01 3.94837e+01
Total Energy Temperature Pressure (bar) Cons. rmsd ()
7.23430e+01 3.65290e+02 4.25425e+01 3.43881e-07
II) from gmxdump
ffparams:
atnr=5
ntypes=40
functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05
functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05
functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07
functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06
functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[20]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB=
1.14000e+02, ctB= 5.19650e+02
functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB=
1.12000e+02, ctB= 4.18220e+02
functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB=
1.12000e+02, ctB= 5.02190e+02
functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB=
1.09470e+02, ctB= 4.19050e+02
functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB=
1.08500e+02, ctB= 4.60620e+02
functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01,
rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00,
rbcB[3]=-2.63176327e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01,
rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01,
rbcB[3]=-2.56062469e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00,
rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00,
rbcB[3]=-1.85645523e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01,
rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00,
rbcB[3]=-3.34730682e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00,
rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01,
rbcB[3]=-6.25015497e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[35]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B=
0.00000000e+00, c12B= 0.00000000e+00
functype[36]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01
functype[37]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02
functype[38]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01
functype[39]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01
fudgeQQ = 0.5
I have several reasons to believe that gromacs dont give the right results
although it "understands" the values of my input top file. the model i use is
Trappe and my colleague researcher which use the exact model of this molecule
finds different results from mine. the fact that the results from my fellow
colleague are accepted as standards in this lab plus the positive total energy
of mine and abnormal value of density (0.96 gr/ml) i take from my results
brought me to the conclusion that smth is wrong in gromacs.
Please
knowing that this isnt your concern and you offer your help without effort
encourage me to continue to this project and understand the way that gromacs
works. believe me that i have been working hard on this and these are not words
of someone lazy who wants the work to be done by smone else.
i think it is is smth simple that i miss here and i call your experience on
this problem.
if you want more details i will do whatever i can to give it to you.
thank you
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