[gmx-users] analysis of MD energy terms
Moeed
lecielll at googlemail.com
Fri May 28 01:18:32 CEST 2010
Hello Justin,
[Actually, the reason I posted some parts of my mdp file was because you
said I am sending redundant information so I just deleted the first lines of
mdp file :) ]
To get the xtc file initially I used nrexcl=3 in the top file. Then I used
mdrun -rerun to breakdown energies on this xtc file with new top file nrexcl=7
to exclude all intramolecular nonbonded interactions (you definitely recall
all these details :)
1- Does it matter in the first run (to get xtc) what option I use for nrexcl
in top file. Actually, I thought maybe in the normal run I have to set this
option to zero. I did that and I got lincs warning (the same applies
for nrexcl=1).
So I tried nrexcl=2 and I noticed the results are not the same as nrexcl 3.
However, this means I am still having nonbonded intramolecular interaction
between atoms that are less than 2 bonds away. Am I right?
2- I am wondering why in this breakdown I still see LJ and coloumb 1-4
interactions while I have nrexcl=2.
3- In the second set of results (nrexcl=3) potential energy is 2766 > 2156
(the value for nrexcl==2). Logically, when 3 bonds away are excluded
potential energy should be less I think!..
4- Regarding the units, in chapter 2 of manual the units for energy is in
KJ/mol. Here is this table I see heat capacity is given in J/mol K. Could
you please kindly tell me the units what is the unit for energy temrs LJ or
coulomb?
5- Very important question: If I want to compute the interaction energies
BETWEEN molecuels, do I have to sum up LJ (SR) =(-3026 e.g) and coloumb
(SR)=74 ? and can I conclude that there is a net attraction energy in the
system?
6- If I want to assure that equilibrium is reached, can I make the
simulation time long enough such that T reaches 300 K? now it is 297 K.
I appreciate your help.
Thanks
Moeed
*mdrun -rerun on trajectory for nrexcl=2 in top file*
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 4286.19 258.765 231.378 40.1269
401.349
Ryckaert-Bell. 722.966 69.0616 61.1677 11.1046
111.068
*LJ-14 498.432 31.2891 30.9138 1.67344
16.7378*
* *
*Coulomb-14 -322.264 11.5056 10.1507 1.87612
18.765*
* *
*LJ (SR) -3026.03 45.5198 38.6106 8.35011
83.5178*
* *
*Coulomb (SR) 74.4564 2.53605 2.53537 0.02034
0.203441*
Coul. recip. -77.5276 2.3709 1.31777 -0.682623
-6.8276
Potential 2156.22 335.429 282.807 62.4689
624.814
Kinetic En. 0 0 0 0
0
Total Energy 2156.22 335.429 282.807 62.4689
624.814
Temperature 0 0 0 0
0
Pressure (bar) 1563.28 161.924 161.475 4.17097
41.718
Cons. rmsd () 0 0 0 0
0
Mu-X -0.00385475 0.893851 0.893682 -0.00602335
-0.0602456
Heat Capacity Cv: nan J/mol K (factor = nan)
*
*
*mdrun -rerun on trajectory for nrexcl=3 in top file*
Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 14 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
Mu-X -0.0523974 0.826473 0.826318 -0.00553723
-0.0553834
Heat Capacity Cv: nan J/mol K (factor = nan)
; 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
nstxtcout = 10
; 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
pbc=xyz
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