On 29 February 2012 14:04, Mark Abraham <mark.abra...@anu.edu.au> wrote:
> 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. > > Yes, I am sorry, I forgot to mention that in that case I use dt=0.001 and nsteps=5000000. > 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: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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