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 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
