[gmx-users] remd ... is it exchanging?
David van der Spoel
spoel at xray.bmc.uu.se
Mon Aug 28 19:43:01 CEST 2006
Carsten Baldauf wrote:
> ok, i got it wrong ...
> i see now my problem ... i am using an extremely big box ...
> the length of my fully extended peptide is about 5.6 nm i will try a box
> with an image distance of 5.7 nm.
> this should more or less resemble the status of your input, am i right?
In fact we had very (too) little water, and were we to do the
simulations again we would use more. When your peptide collapses in
solvent it will be smaller, but at high T it may still be slightly
extended. I'd suggest doing a short test sim at high T (but not higher
than the boiling point...) to see how large you need to take the box.
I'd also suggest not using higher than 373 K, at least if you want to
interpret the data at high T as well. If you want to use REMD solely for
sampling at lower T you can use unphysically T as well (unphysical
because the water does not evaporate at T > 373 in the simulation).
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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