[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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