[gmx-users] energy problems
Osmany Guirola Cruz
osmany.guirola at cigb.edu.cu
Thu Oct 7 17:26:28 CEST 2004
Hi
I am doing a simulation of a short peptide in water with counterions Tcoup
Pcoup ..... but i do a graph of the total energy and this is the result
t(ps) Potencial Kinetic Total Temp
0.000000 -123848.714738 24317.926256 -99530.788482 303.036540
0.200000 -128255.528122 26093.377899 -102162.150223 325.161236
0.400000 -128604.439218 25163.987820 -103440.451398 313.579691
0.600000 -129228.424209 24885.526342 -104342.897868 310.109658
0.800000 -129548.890008 24847.294010 -104701.595998 309.633228
1.000000 -129836.118295 25133.901220 -104702.217076 313.204769
.............................................
.......................................
etc
In the total energy there it's a great jump from the step(0) to the next(0.2)
similar in the potencial. (after this it oscillate around the averge). is
this correct? or i have something wrong in my mdp files
My TCoup=300 but g_energy say that the average is 314 that it's greater than
the expected value 300. Why?
here my mdp file
title = fws
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 5000000
nstcomm = 1
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlist = 10
ns_type = grid
energygrps = Protein SOL
rlist = 0.8
;coulombtype = PME
rcoulomb = 1.4
rvdw = 0.8
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc_grps = protein sol CL-
ref_t = 300 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
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