That would be the right choice for the GROMOS43 ff series. In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. Never believe what is written in a manual :)) It is always better to keep the values that are used for parameterization (the one I gave you) when using a force field. The idea that bigger = better does not work ... you change the balance of forces and thus the properties of the force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers) would describe the simulation setup: no need of the manual for this. I looked in some older papers but found no values for epsilon_r and _rf. From older posts of this mailing list I got the impression that epsilon_r = 1 and epsilon_rf the value of the relative permitivity of the medium. In the case of a simulation in vacuum epsilon_rf would be also 1 and then I have no correction from the reaction field, also grompp tells me that epsilon_r = epsilon_rf would be meaningless with a reaction field. So I'm puzzeld.Thanks for an answer Thomas _______________________________________________ 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 If both epsilon values have the same value, is it then equal to normal cut-offs (type = cut-off)? Sorry for the many questions. Thomas |
_______________________________________________ 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
