[gmx-users] (no subject)

[Justin A. Lemkul]

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

-- 
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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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