Yang Ye wrote:
On 9/11/2007 7:05 AM, WU Yanbin wrote:
Hey, Everyone,
Question about options for grompp command:
(1) "check14": the description is "Remove 1-4 interactions without
Van der Waals". What's the meaning by "Van der Waals"? Does it mean if
there is no corresponding Van der Waals parameter defined in [
pairtypes ], the item in [ pairs ] would be removed?
Yes. From your later sentence, I think that you got what VDW means.
So when the pair parameters are zero the interactions are not
calculated, according to the GROMACS philosophy that we don't compute
anything if we know the result is zero in advance.
(2) "shuffle": Is it compulsory for parallel running? I read from
the manual that it's a must.
No, although it helps it. It needs to be used together with sort.
Shuffle helps especially for mixed systems like membranes. Sort should
be used with caution since it is difficult to unsort (whereas unshuffle
is possible). These options will both disappear in gromacs 4.0
Thanks in advance.
Yours Sincerely,
WU Yanbin
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David.
________________________________________________________________________
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
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