2016-02-08 17:40 GMT-07:00 Alireza Moradzadeh <[email protected]>: > Dear Christoph, > > Thank you for your email. But I encountered problem with implementation of > it. I want to use PME as my coulomb type. So I have to put my three bead > molecule beads in different charge groups. But I face severe problem with > electrostatic interaction between beads which blows up my system. I am > seeking a way to equilibrate this system.
If you need to combine PME with tabulated interactions, you might need to start from a different initial guess for the potentials, because the Boltzmann inversion of the g(r) contains contributions from the coulombic part, too. I would use a couple of pure LJ interactions for a start (put them as NAME.pot.in in the same directory as settings.xml). Christoph > Thanks > Alireza >> On Feb 8, 2016, at 10:28 AM, Christoph Junghans <[email protected]> wrote: >> >> 2016-02-07 19:50 GMT-07:00 Alireza Moradzadeh <[email protected]>: >>> Dear Users, >>> >>> Let's suppose I have two molecules one composed of three beads and the >>> second one composed of just one bead. mol1 : A B C & mol2 : D >>> what's is the number of energy groups in gromacs. should it be like: mol1 >>> mol2 and energygrp_table: mol1 mol1 mol1 mol2 mol2 mol2 or A A A B A C A D >>> B B B C B D C C C D >> Yes, that is correct! >> >>> >>> Thanks, >>> Alireza >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send an >>> email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at https://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "votca" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/votca/mhHPMe4CDIg/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
