[gmx-users] How to reduce high repulsion from system?
Moeed
lecielll at googlemail.com
Thu Apr 29 22:02:24 CEST 2010
Dear experts,
Could you please take a look at energy values. The system contains only
stack of hexane molecules. MD sun gives lincs warning.
1- How can I get rid of high repulsive potential?
*genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o
Hexane-stack.gro*
********------------------------***************************************************************************
energy minimization
my output.mdrun_em:
Steepest Descents converged to Fmax < 1000 in 30 steps
Potential Energy = 4.76092783832156e+05
Maximum force = 9.86600079729483e+02 on atom 3115
Norm of force = 5.33725886931530e+02
*********************************************************************************************************
g_energy file:
Statistics over 61 steps [ 0.0000 thru 0.1200 ps ], 12 data sets
All averages are exact over 61 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
------------------------------
-------------------------------------------------
Angle 78416.5 38731.2 25083.3 838187
102231
LJ-14 1.16009e+08 8.87401e+08 8.87401e+08 3.06025e+06
373250
Coulomb-14 734.065 480.683 140.481 13056.3
1592.44
LJ (SR) 5482.29 5991.07 4445.16 114080
13914.1
Coulomb (SR) 1711.47 732.288 228.708 -19758
-2409.83
Potential 1.16326e+08 8.8739e+08 8.8739e+08 921124
112347
Kinetic En. 1.77327e+18 5.4851e+18 4.28286e+18 9.73294e+19
1.1871e+19
Total Energy 1.77327e+18 5.4851e+18 4.28286e+18 9.73294e+19
1.1871e+19
Temperature 4.06507e+16 1.25741e+17 9.81811e+16 2.2312e+18
2.72133e+17
Pressure (bar) 1.48406e+15 4.59052e+15 3.58436e+15 8.14557e+16
9.93493e+15
T-HEX 4.06507e+16 1.25741e+17 9.81811e+16 2.2312e+18
2.72133e+17
Lamb-HEX 0.99144 0.00206848 0 -0.0617392
-0.00753016
Heat Capacity Cv: -0.934076 J/mol K (factor = 9.56799)
***************
*************************************************************************
title = Hexane
cpp = /lib/cpp
; Run control
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 1.0 ps.
nstcomm = 1 ; frequency for center of mass motion
removal
; Output control
nstenergy = 10 ; frequency to write energies to energy
file. i.e., energies and other statistical data are stored every 10 steps
nstxout = 10 ; frequency to write
coordinates/velocity/force to output trajectory file
nstvout = 0
nstfout = 10
nstlog = 10 ; frequency to write energies to log file
; Neighbor searching
nstlist = 10 ; neighborlist will be updated at least
every 10 steps
;ns_type = grid
; Electrostatics/VdW
coulombtype = cut-off
vdw-type = cut-off
; Cut-offs
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Temperature coupling Berendsen temperature coupling is on in two
groups
Tcoupl = berendsen
tc-grps = HEX ;sol
tau_t = 0.1 ;0.1
ref_t = 300 ;300
; Pressure coupling: Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Velocity generation Generate velocites is on at 300 K. Manual
p155
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = lincs
pbc=xyz
****************************************************************************************
;
; File 'Hexane.top' was generated
; By user: moeed (500)
; On host: moeed-desktop
; At date: Thu Apr 8 13:51:19 2010
;
; This is your include topology file
; Generated by x2top
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
HEX 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot
-0.18
2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot
-0.3
3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot
-0.42
4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot
-0.54
5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot
-0.66
6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot
-0.84
7 opls_140 1 HEX H1 6 0.06 1.008 ; qtot
-0.78
8 opls_140 1 HEX H2 6 0.06 1.008 ; qtot
-0.72
9 opls_140 1 HEX H3 6 0.06 1.008 ; qtot
-0.66
10 opls_140 1 HEX H4 5 0.06 1.008 ; qtot
-0.6
11 opls_140 1 HEX H5 5 0.06 1.008 ; qtot
-0.54
12 opls_140 1 HEX H6 4 0.06 1.008 ; qtot
-0.48
13 opls_140 1 HEX H7 4 0.06 1.008 ; qtot
-0.42
14 opls_140 1 HEX H8 3 0.06 1.008 ; qtot
-0.36
15 opls_140 1 HEX H9 3 0.06 1.008 ; qtot
-0.3
16 opls_140 1 HEX H10 2 0.06 1.008 ; qtot
-0.24
17 opls_140 1 HEX H11 2 0.06 1.008 ; qtot
-0.18
18 opls_140 1 HEX H12 1 0.06 1.008 ; qtot
-0.12
19 opls_140 1 HEX H13 1 0.06 1.008 ; qtot
-0.06
20 opls_140 1 HEX H14 1 0.06 1.008 ; qtot
0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
1 18 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
1 19 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
1 20 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
2 3 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
2 16 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
2 17 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
3 4 1 1.540000e-01 4.000000e+05 1.540000e-01 4.000000e+05
3 14 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
3 15 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
4 5 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
4 12 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
4 13 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
5 6 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
5 10 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
5 11 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 7 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 8 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 9 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 14 1
1 15 1
2 5 1
2 12 1
2 13 1
3 6 1
3 10 1
3 11 1
3 18 1
3 19 1
3 20 1
4 7 1
4 8 1
4 9 1
4 16 1
4 17 1
5 14 1
5 15 1
6 12 1
6 13 1
7 10 1
7 11 1
8 10 1
8 11 1
9 10 1
9 11 1
10 12 1
10 13 1
11 12 1
11 13 1
12 14 1
12 15 1
13 14 1
13 15 1
14 16 1
14 17 1
15 16 1
15 17 1
16 18 1
16 19 1
16 20 1
17 18 1
17 19 1
17 20 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 18 1 1.120000e+02 4.000000e+02 1.120000e+02
4.000000e+02
2 1 19 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
2 1 20 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
18 1 19 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
18 1 20 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
19 1 20 1 1.080000e+02 4.000000e+02 1.080000e+02
4.000000e+02
1 2 3 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
1 2 16 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
1 2 17 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
3 2 16 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
3 2 17 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
16 2 17 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
2 3 4 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
2 3 14 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
2 3 15 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
4 3 14 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
4 3 15 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
14 3 15 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
3 4 5 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
3 4 12 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
3 4 13 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
5 4 12 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
5 4 13 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
12 4 13 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
4 5 6 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
4 5 10 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
4 5 11 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
6 5 10 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
6 5 11 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
10 5 11 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
5 6 7 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
5 6 8 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
5 6 9 1 1.120000e+02 4.000000e+02 1.120000e+02
4.000000e+02
7 6 8 1 1.080000e+02 4.000000e+02 1.080000e+02
4.000000e+02
7 6 9 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
8 6 9 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
18 1 2 3 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
1 2 3 4 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
2 3 4 5 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
3 4 5 6 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
4 5 6 7 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
[ system ]
; Name
HEX
[ molecules ]
; Compound #mols
HEX 256
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