On 29/02/2012 8:33 PM, Thomas Evangelidis wrote:
Dear GROMACS community,
I use the following parameters to run MD of ethane in vacuo. Then I
calculate the H-C-C-H dihedral angle distribution and from that the
rotational energy barrier using the formula DeltG=-k*T*ln(x), where x
is the dihedral value. The rotational energy barrier is correct (~ 12
kJ) with all-bond constraints, but not with h-bond or no bond
constraints. Could anyone tell me which other parameters to tweak in
order to get the correct dihedral angle distribution without any bond
constraints.
Thanks in advance.
Thomas
integrator = md
tinit = 0.0
dt = 0.002
This is too long if you are not using all-atom constraints. See manual
6.5 for discussion.
Mark
nsteps = 2500000
init_step = 0
simulation_part = 1
comm-mode = Angular
nstcomm = 20
comm-grps =
emtol = 0.01
emstep = 0.01
niter = 0
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 500
nstcalcenergy = -1
nstenergy = 500
nstxtcout = 100
xtc-precision = 1000
xtc-grps =
energygrps = System
nstlist = 0
ns_type = simple
pbc = no
periodic_molecules = no
rlist = 0
rlistlong = -1
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 0.0
epsilon_r = 1.0
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 0
DispCorr = no
table-extension = 1
energygrp_table =
implicit_solvent = No
tcoupl = v-rescale
nsttcouple = 5
nh-chain-length = 10
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = no
Pcoupltype = Isotropic
nstpcouple = -1
tau_p = 1
compressibility =
ref_p = 1.0 1.0 1.0
refcoord_scaling = No
andersen_seed = 815131
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
constraints = all-bonds
constraint-algorithm = Lincs
continuation = no
Shake-SOR = no
shake-tol = 1e-04
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
morse = no
--
======================================================================
Thomas Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece
email: [email protected] <mailto:[email protected]>
[email protected] <mailto:[email protected]>
website: https://sites.google.com/site/thomasevangelidishomepage/
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