# [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

```