[gmx-users] TFE-water simulations
spoel at xray.bmc.uu.se
Tue Apr 29 21:35:01 CEST 2003
On Tue, 2003-04-29 at 20:55, Attila Borics wrote:
> 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
You haven't specified tau_p . I t should be >= 1 ps.
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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