David van der Spoel
spoel at xray.bmc.uu.se
Sat Jan 13 16:22:19 CET 2007
Dmitriy Golubobsky wrote:
> Dear Guru;
> Please give any suggestion or hint on this problem
> I do MD for a polymer chain (about 1000 atoms) in water (SPC) with OPLSAA
> according to the alogoritm
> 1 em in vacoom
> 2. solvate with water
> 3. do em and position restrain
> 4. do NVT MD with berendsen thermostan
> with dt=0.001ps and trajectory length 5ns
> Coulomb, VdW=cut-off
> the aim of simulation is to find coil to globule transition
> I do NVT under different temperatures (from 280 to 340 K)
> and really find the temperature after what my polymer become a globule
> (about 310 K)
> it was the result that i expact =)
> but when I do MD with the temperature 315-everything is ok,it is a
> globule, 320-ok.
> but with the higher tempetature it's didn't become a globule. and it's
> not what i'm expacting.
> may be where is a mistake in my algorithm.
> perhaps i've to do an annealing MD or something else?
First your simulations may be too short. You could try REMD in this
temperature range, then make sure everything equilibrates and compute a
melting curve, which is probably what was measured.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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