Dear users,
I have performed an simulation of polypeptide(5-residues of
alanine) in vacuum using gmx_4.5.5 (Double Precision). For this, I am using
all cutoff=0 with no pbc. The input mdp file for the simulation is given
below
title = peptide in vaccum
cpp = /lib/cpp
define = -DFLEXIBLE
; RUN CONTROL
integrator = md
comm_mode = ANGULAR
nsteps = 1000000
dt = 0.0005
; NEIGHBOR SEARCHING
nstlist = 0
ns_type = simple
pbc = no
rlist = 0
; OUTPUT CONTROL
nstxout = 1000
nstvout = 1000
nstxtcout = 0
nstlog = 1000
constraints = none
nstenergy = 1000
; OPTION FOR ELECTROSTATIC AND VDW
rcoulomb = 0
; Method for doing Van der Waals
rvdw = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl = V-rescale
tc_grps = Protein
tau_t = 0.1
ref_t = 300
The output (.log) file is
Step Time Lambda
0 0.00000 0.00000
Group rest with mass 4.28491e+02, Ekrot 6.48028e+00 Det(I) = 4.27209e+03
COM: 1.82773 1.85017 1.82461
P: 0.00000 -0.00000 0.00000
V: 0.00000 -0.00000 0.00000
J: -0.82095 -13.54870 -19.02024
w: 0.02012 -0.41432 -0.38715
Inertia tensor (3x3):
Inertia tensor[ 0]={ 1.34454e+01, -6.11374e+00, 2.21534e+00}
Inertia tensor[ 1]={-6.11374e+00, 2.88115e+01, -6.31417e+00}
Inertia tensor[ 2]={ 2.21534e+00, -6.31417e+00, 1.36527e+01}
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
4.93368e+00 1.49038e+01 1.00713e+00 3.83183e+01 7.57789e+01
Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.
7.82758e+02 -6.47030e+01 -1.48187e+03 -6.28870e+02 2.30892e+02
Total Energy Conserved En. Temperature Pressure (bar)
-3.97978e+02 -3.97978e+02 3.08553e+02 0.00000e+00
gen_vel = yes
gen_temp = 300
Now the problem is with Coulomb (SR) value.To check this value, I have
calculated coulomb interactions beyond 1-4 interaction by the following
equation
energ=(f*q1*q2)/r ; where f=138.935485
but the value which I obtain for step 0 is -170.10733 and this not the same
as the log file. I do not know how Gromacs calculate coulomb (SR) value.
Please suggest if I am missing something.
Thanks
Santu
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