[gmx-users] Re. genbox -shell
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 15 22:09:46 CET 2005
Mark Abraham wrote:
> Dongsheng Zhang wrote:
>> Dear David,
>> I am confused by your reply. In your tutorial, you use
>> editconf .. -c -d 0.5
>> Now I am using -d 1.0, and 1.0 nm = 10 A, I don't understand why you
>> think the box is too small.
> A pertinent question is whether your shell is large enough to model
> long-range electrostatics reasonably. I suspect you'd have a heavy
> majority of people in this decade thinking that 1.0nm is not enough.
but this was an extended peptide, and it will collapse. Good way to make
a starting structure for folding simulations.
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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://xray.bmc.uu.se/~spoel
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