Hi Alireza, Have you excluded interactions between bonded beads? One of your CG molecule has 3 CG beads, so try excluding non-bonded interactions among them and see if that works for you. You can use gromacs [exclusions] setting in your topology to exclude the interactions.
Best, Sikandar On Tue, Feb 9, 2016 at 2:20 PM, Alireza Moradzadeh <[email protected]> wrote: > 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. > -- 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.
