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
list..
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
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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