[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Wed May 16 14:55:00 CEST 2012
On 5/16/12 8:49 AM, rama david wrote:
> Hi Gromacs Friends,
> I plan to simulate protein In Trifluoro Ethanol solvent
> using G96 53a6 FF
> Please help to define parameters in md.mdp
> For water I am using following mdp file ....
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 0.9 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
> vdw-type = Cut-off
> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME
> For TFE and water mix of different conc , What should be the mdp file
> parameter ???
> I am using following ones..
> Twin range cutt-off for nnonbonded interactions..
> Short range cut-off 0.8 and long range 1.4 for both
> coulombic and lennard-jones
> Short range updates for every 5 step togather with pair
> Please give me valuable suggestion ..
The settings given in an .mdp file are dependent upon the force field, not the
molecules in the system. So if you have water or water/TFE, the requirements of
the force field are still the same.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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