[gmx-users] analysis of md run results
Moeed
lecielll at googlemail.com
Wed May 26 21:04:31 CEST 2010
Hello Justin,
The energy values I get differ mainly for LJ and coulomb(SR) terms. I read
through chapter 4 of manual but I did not find the difference between
LJ/coulomb 1-4 and SR.
1-Where can I read about the differences of these?
2-Do you think the difference in energies as a result of excluding
intramolecualr nonbonded interactions are reasonable?
3-I can not figure out why pressure in the first case in negative and it is
very large when exclusions are included.Also in the second case kinetic
energy is zero. :(
4-If I want to perform NPT simulation, the only thing I need to do is to
switch on Pcoupl option in mdp file?
Thank you for your help.
No exclusions: mdrun -s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr* -x
trajectoy.xtc *-c Hexane-Stack125_after_md -v >& output.mdrun_md
g_energy -f ener.edr -o energy.xvg:
tatistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 13 data sets
The term 'Cons. rmsd ()' is averaged over 501 frames
All other averages are exact over 5001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 4400.14 259.533 194.602 59.4737
594.856
Ryckaert-Bell. 1000.11 115.318 88.7683 25.494
254.991
LJ-14 648.7 37.6872 36.5595 3.16904
31.6967
Coulomb-14 -281.387 32.3948 12.468 10.3554
103.574
*LJ (SR) -3322.54 46.1011 40.9609 7.32669
73.2816
Coulomb (SR) 667.867 26.5968 9.4795 -8.60663
-86.0835*
Coul. recip. 921.791 26.6407 8.48573 -8.74618
-87.4793
*Potential 4034.68 386.493 290.055 88.466
884.837*
Kinetic En. 6336.76 250.507 237.567 27.5244
275.299
Total Energy 10371.4 561.13 450.23 115.99
1160.14
Temperature 297.592 11.7645 11.1568 1.29262
12.9288
P*ressure (bar) -37.0417 1165.58 1161.54 -33.5839
-335.906*
Cons. rmsd () 3.74741e-06 2.92095e-07 2.34721e-07 6.02133e-08
6.02253e-07
Heat Capacity Cv: 12.5011 J/mol K (factor = 0.00156281)
run with exclusions in top file: mdrun -*rerun trajectoy.xtc* -s
Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c Hexane-Stack125_after_md
-v >& output.mdrun_md
Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 13 data sets
All averages are over 501 frames
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 4400.09 284.259 237.268 54.2184
542.293
Ryckaert-Bell. 1009.62 124.468 94.0379 28.2417
282.474
LJ-14 648.411 40.6844 39.926 2.70793
27.0848
Coulomb-14 -278.654 34.4227 11.8071 11.1987
112.01
*LJ (SR) -3010.16 47.968 42.5388 7.67736
76.789
Coulomb (SR) 74.7846 2.5186 2.47007 0.170417
1.70451*
Coul. recip. -78.0436 2.58606 1.54725 -0.717662
-7.17805
Potential 2766.05 454.268 342.141 103.497
1035.18
Kinetic En. 0 0 0
0 0
Total Energy 2766.05 454.268 342.141 103.497
1035.18
*Temperature 0 0 0
0 0
Pressure (bar) 1973.01 177.068 172.803 13.3792
133.819*
Cons. rmsd () 0 0 0
0 0
Heat Capacity Cv: nan J/mol K (factor = nan)
with: mdp file
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
pbc=xyz
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