[gmx-users] energy break down
Moeed
lecielll at googlemail.com
Thu May 20 00:35:50 CEST 2010
Hello,
I am trying to get only interaction energies (vdw and electrostatics)
between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in
the system. I have added *exclusions section* at the end of top file to
exclude all nonbonded interactions between atom 1 and all other 20 atoms.
Unfortunately, I still have problem monitoring the breakdown of energies.
grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-excl.top -o
Hexane-Stack125_em >& output.grompp_em
mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c Hexane-Stack125_b4pr -v
>& output.mdrun_em
grompp -f md19 -c Hexane-Stack125_b4pr -p Hexane-Stack125-excl.top -o
Hexane-Stack125_md >& output.grompp_md
*mdrun -rerun -*s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c
Hexane-Stack125_after_md -v >& output.mdrun_md
-------------------------------------------------------
Program g_energy, VERSION 4.0.7
Source code file: enxio.c, line: 283
Fatal error:
Energy file ener.edr not recognized, maybe different CPU?
*******em output:
Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy = -1.06286703814635e+03
Maximum force = 2.02809790403662e+02 on atom 1183
Norm of force = 1.41349547097082e+02
********md output
Program mdrun, VERSION 4.0.7
Source code file: gmxfio.c, line: 737
Can not open file:
rerun.xtc
md.mdp
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
energygrps = Hexane Hexane
; Neighbor searching
nstlist = 10 ; neighborlist will be updated at least
every 10 steps
;ns_type = grid
; Electrostatics/VdW
coulombtype = PME
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
*; Energy group exclusions
eneegygrp_excl = HEX *
pbc=xyz
/*********************topology file:
;
; File 'Hexane-PRODRG.top' was generated
; By user: moeed (500)
; On host: moeed-desktop
; At date: Tue May 11 09:31:28 2010
;
; This is your topology file
; "Everything He Lacks, He Makes Up In Denial" (Offspring)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Hexane 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_140 1 HEX H11 1 0.06 1.008 ; qtot
-0.12
3 opls_140 1 HEX H12 1 0.06 1.008 ; qtot
-0.06
4 opls_140 1 HEX H13 1 0.06 1.008 ; qtot
0
5 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot
-0.12
6 opls_140 1 HEX H21 2 0.06 1.008 ; qtot
-0.06
7 opls_140 1 HEX H22 2 0.06 1.008 ; qtot
0
8 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot
-0.12
9 opls_140 1 HEX H31 3 0.06 1.008 ; qtot
-0.06
10 opls_140 1 HEX H32 3 0.06 1.008 ; qtot
0
11 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot
-0.12
12 opls_140 1 HEX H41 4 0.06 1.008 ; qtot
-0.06
13 opls_140 1 HEX H42 4 0.06 1.008 ; qtot
0
14 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot
-0.12
15 opls_140 1 HEX H51 5 0.06 1.008 ; qtot
-0.06
16 opls_140 1 HEX H52 5 0.06 1.008 ; qtot
0
17 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot
-0.18
18 opls_140 1 HEX H61 6 0.06 1.008 ; qtot
-0.12
19 opls_140 1 HEX H62 6 0.06 1.008 ; qtot
-0.06
20 opls_140 1 HEX H63 6 0.06 1.008 ; qtot
0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 8 1
8 9 1
8 10 1
8 11 1
11 12 1
11 13 1
11 14 1
14 15 1
14 16 1
14 17 1
17 18 1
17 19 1
17 20 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 9 1
1 10 1
1 11 1
2 6 1
2 7 1
2 8 1
3 6 1
3 7 1
3 8 1
4 6 1
4 7 1
4 8 1
5 12 1
5 13 1
5 14 1
6 9 1
6 10 1
6 11 1
7 9 1
7 10 1
7 11 1
8 15 1
8 16 1
8 17 1
9 12 1
9 13 1
9 14 1
10 12 1
10 13 1
10 14 1
11 18 1
11 19 1
11 20 1
12 15 1
12 16 1
12 17 1
13 15 1
13 16 1
13 17 1
15 18 1
15 19 1
15 20 1
16 18 1
16 19 1
16 20 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 8 1
6 5 7 1
6 5 8 1
7 5 8 1
5 8 9 1
5 8 10 1
5 8 11 1
9 8 10 1
9 8 11 1
10 8 11 1
8 11 12 1
8 11 13 1
8 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
11 14 15 1
11 14 16 1
11 14 17 1
15 14 16 1
15 14 17 1
16 14 17 1
14 17 18 1
14 17 19 1
14 17 20 1
18 17 19 1
18 17 20 1
19 17 20 1
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 5 6 3
2 1 5 7 3
2 1 5 8 3
3 1 5 6 3
3 1 5 7 3
3 1 5 8 3
4 1 5 6 3
4 1 5 7 3
4 1 5 8 3
1 5 8 9 3
1 5 8 10 3
1 5 8 11 3
6 5 8 9 3
6 5 8 10 3
6 5 8 11 3
7 5 8 9 3
7 5 8 10 3
7 5 8 11 3
5 8 11 12 3
5 8 11 13 3
5 8 11 14 3
9 8 11 12 3
9 8 11 13 3
9 8 11 14 3
10 8 11 12 3
10 8 11 13 3
10 8 11 14 3
8 11 14 15 3
8 11 14 16 3
8 11 14 17 3
12 11 14 15 3
12 11 14 16 3
12 11 14 17 3
13 11 14 15 3
13 11 14 16 3
13 11 14 17 3
11 14 17 18 3
11 14 17 19 3
11 14 17 20 3
15 14 17 18 3
15 14 17 19 3
15 14 17 20 3
16 14 17 18 3
16 14 17 19 3
16 14 17 20 3
; Include Position restraint file
;#ifdef POSRES
;#include "posre.itp"
;#endif
; Include water topology
;#include "spc.itp"
;#ifdef POSRES_WATER
; Position restraint for each water oxygen
;[ position_restraints ]
; i funct fcx fcy fcz
; 1 1 1000 1000 1000
;#endif
; Include generic topology for ions
;#include "ions.itp"
[ system ]
; Name
Hexane
[ molecules ]
; Compound #mols
Hexane 125
*[ exclusions ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*
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