Dear Sir, I'm absolutely aware that gromacs uses nm for distance. The values should be 0.556 and 0.89. I used them only for reference purposes and I hope that this didn't cause any misanderstanding so as to point me to the manual. If this is the case of not understanding my questions, I deeply appologize.
Yours Sincerely, Nikos --- David van der Spoel <[EMAIL PROTECTED]> schrieb: > > > On Wed, 12 Dec 2007, Claus Valka wrote: > > > Dear Sir, > > > > I would try to be more precise. > > > > example1 mdp file: > > rlist = (greater or equal to rvdw) > > vdw-type = Switch > > rvdw-switch=5.56 > > rvdw=8.9 > > > are you aware that gromacs usues nm for distance? > > you can find the functional form of the shift/switch > function in the > manual. > > > Between the value 5.56 and 8.9 gromacs uses cubic > > spline? > > > > example2 mdp file: > > > > rlist=5.56 > > vdw-type = Cut-off > > rvdw-switch=0 (this value here should be > irrelevant) > > rvdw=8.9 > > > > Gromacs uses cubic spline after the value 8.9 till > LJ > > to go to zero? > > > > And which is the difference of rlist if someone > uses > > vdw-type = Cut-off instead of vdw-type = Switch? > It > > would have been nice to have images of these > options > > so as to be better understood. > > Because it is stated in the manual: > > rlist: (1) [nm] > > cut-off distance for the short-range neighbor list > > and also: > > Switch > > ...The neighbor search cut-off rlist should be 0.1 > to > > 0.3 nm LARGER than rvdw... > > Isn't this a little bit contradictive? > > > > As far as twin cutoffs are concerned if we want to > > find out the total energy of the non bonded > > interactions we have to add LJ-14 + LJ(SR) + > LJ(LR)? > > > > With tabulated potentials can I use different > cutoffs > > for different types of atoms? Judging from your > answer > > about system wide cutoffs I understand that even > > though I might use tabulated potentials, I won't > be > > able to use different cutoffs for the different > types > > of atoms I have. Am I correct? > > > > Yours Sincerely, > > Nikos > > > > > > --- Mark Abraham <[EMAIL PROTECTED]> > schrieb: > > > >> Claus Valka wrote: > >>> Hello, > >>> > >> > >>> 3rd question: Which is the difference between > the > >>> S(hort)R(ange) LJ and LJ 1-4? For me the short > >> range > >>> interactions are the 1-4LJ, yet it seems that > this > >> is > >>> not the case. > >> > >> GROMACS uses twin-range cutoffs (see manual), so > >> LJ-SR is inside the > >> shorter cutoff, and LJ-LR is outside. > >> > >>> 4th question: I want after 1,45*σ till > >>> 2,33*σ to use the cubic spline in such a > way > >> that > >>> the LJ potential will go smoothly to zero at > >>> 2,33σ. If I use the biggest σ I have, > >> then > >>> in the mdp file rvdw-switch=5.56 and rvdw=8.9. > >> Between > >>> these two values does the cubic spline work as a > >>> switch function using vdw-type = Switch ? > >> > >> Please find a way to describe your problem with > >> plain ASCII text. > >> > >>> 5th question: Given the above if I use vdw-type > >>> =Cut-off and rvdw=8.9 then gromacs will use > cubic > >>> spline till the LJ will reach zero for a value > >> greater > >>> than 8.9, yet to me uknown? If this is not the > >> case > >>> how LJ goes to zero with this option? > >> > >> I don't understand what you're asking. > >> > >>> 6th question: If I want to use a quintic spline > >>> between 1,45*σ till 2,33*σ(cut-off > >> value) > >>> for the different combination of atoms(they have > >>> different ε and σ), then should I use > a > >>> tabulated potential? And if I do that which will > >> be > >>> the meaning of cutoffs in the mdp file as I > would > >> like > >>> them to be different for each of the different > >> types > >>> of atoms I have? Can I use different cut-offs > for > >> the > >>> different types of atoms I have? > >> > >> The cut-offs are a system-wide property. > >> > >> Mark > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the > >> list. Use the > >> www interface or send it to > >> [EMAIL PROTECTED] > >> Can't post? Read > >> http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > Jetzt Mails schnell in einem Vorschaufenster > überfliegen. Dies und viel mehr bietet das neue > Yahoo! Mail - www.yahoo.de/mail > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > >> _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php __________________________________ Ihre erste Baustelle? 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