[gmx-users] problem during simulation of dna-protein complex

[Tsjerk Wassenaar]

Hi Nitu,

Energy minimization is only to remove some strain from your system.
You probably don't want to include position restraints there. After
energy minimization you typically run a short MD run in which you use
position restraints such that the protein/DNA doesn't move to much,
but the water can equilibrrate with respect to the protein. Check the
tutorial material linked on the wiki. This stuff is mentioned in all
of them.

Cheers,

Tsjerk

On Wed, Jul 1, 2009 at 2:06 PM, nitu sharma<sharmanitu35 at gmail.com> wrote:
> Dear Tsjerk
>
>                    Thanks for your right suggestion. It works successfully
> for dna-protein complex simulation. i want to ask one more thing , can I use
> parameter file for energy minimisation which i have used for membrane
> protein simulation or can u suggest me what changes I have to make in
> parameter file to use for dna- protein complex simulation.
> the parameter file like this-
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRE_PROTEIN
> constraints         =  none
> integrator          =  steep
> dt                  = 0.002
> nsteps              =  10000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000
> emstep              =  0.0001
>
> nstcomm             =  1
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> vdw-type            = cut-off
> rvdw                =  1.0
> coulombtype         =  PME
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> comm-mode           = Linear
> pbc                 = XYZ
>
> Specially where i have apply position restrain?
>
> Thanking you
> Nitu sharma
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623