[gmx-users] TFE-water simulations

Attila Borics aborics at bif12.creighton.edu
Tue Apr 29 21:07:01 CEST 2003


I was trying to simulate a 12 residue peptide in 50% (v/v) TFE - SPC
solution. I use the TFE model proposed in the following publication:

Fiorini M, Burger K, Mark AE, Roccatano D, J Phys Chem B 104, 2000,

Everything goes fine with the 200ps (!) NVT positionally restrained
dynamics, but when I want to start the full NPT dynamics with pressure
coupling (Berendsen) it just crashes. The crash is due to high pressure
scaling, and the failure of the constraint algorithm (either lincs or
I'm just wondering if it is because the lack of dihedral potentials in
Fiorini et. al.'s model, so the molecule can rotate along the C-C bond.
Or it's just the matter of equlibration???
I did not make any TFE - SPC boxes previously, just added the desired
number of TFE molecules to solvate my peptide and then added SPC using
I used the isothermal compressibility of water (4.5e-5) however this
value for TFE is 1.22e-4. Since it was used in Fiorini's other paper
successfully, I didn't think that it could be a problem...could it?

Fiorini et. al. JACS 2002, 124, 7734-7744

Could someone help me?
Thank you


Attila Borics <aborics at bif12.creighton.edu>

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