[gmx-users] coil-globule

[David van der Spoel]

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
> rlist=1.2
> r_coulomb=1.4
> r_vdw=1.4
> 
> 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.
________________________________________________________________________
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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