[gmx-users] coil-globule

Dmitriy Golubobsky dmitriy.golubovsky at gmail.com
Sat Jan 13 16:21:26 CET 2007

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,
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?

Dmitriy Golubovsky
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