On Mon, Jan 10, 2011 at 11:19 PM, Shesh Nath <sheshnath65.gmail.com> wrote:
> Sir
> I have simulated 40-mer DNA using following NAB program.
>
>
>
> molecule m;
>
>
> m = fd_helix( "abdna", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", "dna" );
> putpdb( "nuc20.pdb", m, "-wwpdb");
>
>
> then using xleap "leaprc.ff99bsc0" I built prmtop and inpcrd files.
> then I did minimization.
>
>
> lastly I start heating using following step
>
>
>
> Stage 1 heating of polyAT 0 to 50K
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=10000, dt=0.0005,
> ntc=2, ntf=2,
> ntt=1, tautp=1.0,
> tempi=0.0, temp0=50.0,
> ntpr=50, ntwx=50,
> ntb=0, igb=0,
> cut=12.
> /
>
>
> but when temperature arrise to 250K ,one strand of DNA is disappeared.
>
What do you mean "disappeared"? For a chunk of a system to truly disappear
in an amber simulation is, I claim, impossible. However, having no details
about how you created your prmtop or what is really happening, it's unlikely
we can be of any further help. A few comments, though:
dt=0.0005 is a very, very small timestep for the protocols that you're
using. Also, the berendsen thermostat (ntt=1) is probably not the best
choice when the Langevin thermostat is available (ntt=3). Also, you're not
heating your system to 250K -- you're heating it to 50K according to your
input file.
I urge you to look through your output files to try and find error messages
and use Google and the Amber mailing archives to see if your issue has
already been asked about and addressed in the past (it's quite likely).
Good luck,
Jason
I want to my heating step is right or wrong.
> Give me suggestions
>
>
>
>
>
>
>
>
> --
> SHESH NATH
> RESEARCH SCHOLAR,
> THEORETICAL CONDENSED MATTER PHYSICS,
> DEPARTMENT OF PHYSICS,
> BANARAS HINDU UNIVERSITY,
> VARANASI-221005
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jan 11 2011 - 07:30:04 PST
