[gmx-users] (no subject)

rama david ramadavidgroup at gmail.com
Wed May 16 14:49:59 CEST 2012

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 ..

Thank you in advance ..

With Best Wishes,
Rama David
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