[gmx-users] dna-simualtions with gromacs

[Justin Lemkul]

On 3/23/13 11:19 AM, amna khan wrote:
> hi .
>
> i want to simulate the DNA in water, all gromacs  force fields does not
> support DNA . so i chose the amber force fields from Gromacs package,
>
> i want to ask , are all remaining steps same for DNA simulations like the
> lyzome example ?
>
> plase help me
>
> i have done till this step
>
> pdb2gmx -ff amber99sb -f DNAAmber.pdb -o DNA2.pdb -p DNA.top -water spce
> -ignh
>
> editconf -bt octahedron -f  DNA2.pdb -o Complex.pdb -d 1.0
> genbox -cp Complex.pdb -cs spc216.gro -o Complex_b4ion.pdb -p DNA.top
>
> grompp -f em.mdp -c Complex_b4ion.pdb -p DNA.top -o Complex_b4ion.tpr
>
> genion -s Complex_b4ion.tpr -o Complex_b4em.pdb –nname Na –nn 8 –g
> trp_ion.log
>
> rest step can i continue from
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
>
> please help me i am stuck at this step
>

Stuck how?  Note that there is no specific procedure that is universally "right" 
in terms of equilibration and simulation length.  You have to use your best 
judgment based on an assessment of the literature and by observing relevant 
quantities in your system.  Also note that the .mdp files provided in my 
tutorial are for OPLS-AA only.  The cutoffs and other settings are inappropriate 
for AMBER force fields (or any other, for that matter).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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