[gmx-users] md in vacuo

[Thomas Evangelidis]

On 29 February 2012 14:04, Mark Abraham <Mark.Abraham at 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: tevang at bioacademy.gr
>
>           tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
>
>
>
> --
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-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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