[gmx-users] Fwd: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.

[David van der Spoel]

On 2011-02-26 10.27, David van der Spoel wrote:
>
> I found your comments in gmx-user communications. I’m using gmx 453,
> with DNA system. Pdb2gmx is ok, but gmx treated each string as protein.
> I used command
>
> pdb2gmx -f new.pdb -o wt.gro -p wt.top -water tip4p
>
> then choose charmm27 ff,
>
> everything looks good. However I found during my md runs, DNA separated.
> System goes to weird. Do I need to remove TER between the paired stands?
>
Could be periodic boundary conditions.
Otherwise your question is not clear. "weird" is ill-defined.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se