Dear GROMACS community,<br><br>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.<br>
<br>Thanks in advance.<br>Thomas<br><br><br><br>integrator = md<br>tinit = 0.0<br>dt = 0.002<br>nsteps = 2500000<br>init_step = 0<br>
simulation_part = 1<br>comm-mode = Angular<br>nstcomm = 20<br>comm-grps = <br>emtol = 0.01<br>emstep = 0.01<br>niter = 0<br>
fcstep = 0<br>nstcgsteep = 1000<br>nbfgscorr = 10<br>nstxout = 0<br>nstvout = 0<br>nstfout = 0<br>nstlog = 500<br>
nstcalcenergy = -1<br>nstenergy = 500<br>nstxtcout = 100<br>xtc-precision = 1000<br>xtc-grps = <br>energygrps = System<br>nstlist = 0<br>
ns_type = simple<br>pbc = no<br>periodic_molecules = no<br>rlist = 0<br>rlistlong = -1<br>coulombtype = Cut-off<br>rcoulomb-switch = 0<br>
rcoulomb = 0.0<br>epsilon_r = 1.0<br>epsilon_rf = 1<br>vdw-type = Cut-off<br>rvdw-switch = 0<br>rvdw = 0<br>DispCorr = no<br>
table-extension = 1<br>energygrp_table = <br>implicit_solvent = No<br>tcoupl = v-rescale<br>nsttcouple = 5<br>nh-chain-length = 10<br>tc-grps = System<br>
tau_t = 0.1<br>ref_t = 300<br>Pcoupl = no<br>Pcoupltype = Isotropic<br>nstpcouple = -1<br>tau_p = 1<br>compressibility = <br>
ref_p = 1.0 1.0 1.0<br>refcoord_scaling = No<br>andersen_seed = 815131<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br>
constraints = all-bonds<br>constraint-algorithm = Lincs<br>continuation = no<br>Shake-SOR = no<br>shake-tol = 1e-04<br>lincs-order = 4<br>lincs-iter = 1<br>
lincs-warnangle = 30<br>morse = no<br><br clear="all"><br><br><br><br>-- <br>
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<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
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