Dear gmx users,
I am running a NPT simulation of Galactose in water for 10ns using united
atom force field on gromacs 3.3.1. The mdp parameters used are:
dt = 0.002
nstcomm = 1
nsteps = 5000000 ; 10 ns (run control)
nstxout = 10000
nstvout = 10000
nstxtcout = 250
nstenergy = 250
energygrps = GLA SOL
nstlist = 10
ns_type = grid
rlist = 1.1 ;(neighbor searching)
coulombtype = PME
;rcoulomb_switch = 1.0
rcoulomb = 1.1
vdwtype = shift
;rvdw_switch = 1.0
rvdw = 1.1
fourierspacing = 0.12 ;(nm)
ewald_rtol = 1e-5
pme_order = 4 ;(electrostatics and VDW)
tcoupl = berendsen
tc_grps = GLA SOL
tau_t = 0.1 0.1
ref_t = 300 300
pcoupl = berendsen
compressibility = 4.5e-5
tau_p = 1.0
ref_p = 1
gen_vel = no
constraints = all-bonds
constraint_algorithm = lincs
After 10 ns i am calculating pressure using g_energy program. Average by
g_energy comes to be arround 0.99 bars while by xmgrace it comes to be 1.4
bars.
I reran the same simulation for 10ns using nstegergy = 1, instead of 250.
this time the average pressure calculated by g_energy and xmgrace was same
i.e. 0.99 bars.
This means that g_energy calculates average using all MD steps i.e. for
pressure values written after every 0.002 ps, while the average of xmgrace
is from pressure values mentioned in .xvg file.
I converted .edr file to a text file, it contained three columns for each
term i.e. energy, av energy and sum energy. for eg :
time: 5.00000e-01 step: 250
Component Energy Av. Energy Sum Energy
G96Angle 2.30488e+01 7.26315e+03 5.68798e+03
Proper Dih. 1.11964e+01 3.20236e+03 2.63734e+03
Improper Dih. 4.14890e+00 2.55975e+03 1.09996e+03
LJ-14 2.02705e+01 3.40112e+03 4.57903e+03
Coulomb-14 4.09736e+01 1.17554e+03 1.09782e+04
LJ (SR) 6.84730e+03 3.30860e+06 1.69561e+06
Coulomb (SR) -4.08518e+04 4.90539e+06 -1.02531e+07
Coul. recip. -2.35144e+03 2.94449e+04 -5.88310e+05
Potential -3.62563e+04 2.58237e+06 -9.12079e+06
Kinetic En. 6.61766e+03 2.14269e+06 1.66692e+06
Total Energy -2.96387e+04 3.00496e+05 -7.45386e+06
Temperature 2.98376e+02 4.35590e+03 7.51579e+04
Pressure (bar) 5.51461e+02 1.30509e+07 6.42281e+04
My question is what these numbers mean and which of these columns are used
by g_energy program to calculate the average values (say average
pressure)??
Even if nstenergy = 250 and edr file has energies written after every 0.5
ps (250 steps), still g_energy calculates average pressure based on
pressure values writen after each MD step i.e. 0.002 ps. why is this so??
Thanxs in advance.
Rashmi
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