In fact, I did the same thing but it worked only for first step then it started to give me LINCS errors. Due to non equilibrated sys.
> On Feb 9, 2016, at 12:24 PM, Christoph Junghans <[email protected]> wrote: > > 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 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.
