2016-02-24 19:45 GMT-07:00 Alireza Moradzadeh <[email protected]>: > Dear All, > > I am working with GROMACS to obtain potential between beads of two > molecules. > Molecule 1 has three beads with partial charges on each bead. > Molecule 2 has only one bead with opposite charge equal to summation of > charge of molecule 1. > > When I use energy groups for gormacs with PME my system blows up unless I > put charges equal to zero on all of beads. > My system works well when I use LJ parameters with PME and LINCS algorithm > I did not find any coarse graining sample for charged molecules. How can I > use table with partial charges on each bead. It seems to me, there is a problem in your setup.
You could try to use the default 12-6 LJ table with your LJ parameters to check if the problem comes from switching to tabulated interactions itself or if it is due to your special table. The default 6-12 table is in /usr/share/gromacs/top/table6-12.xvg. And please note for tables it is easier to use C6/C12 combination rules instead of sigma/eps, which means using combination rule 1 in the [ defaults ] block. VOTCA only uses the C12 (6th & 7th) columns for iterating interactions and hence it doesn't matter (in an IBI setup) what value C6 has and C12 just act as a global scaling parameter, which we usually set to 1. So in some sense VOTCA's table are simpler column 1: r column 2-5: doesn't matter, so put 0 column 6+7; potential + derivative To convert table6-12.xvg to a VOTCA style table column 6 would C6*(column 4) + C12*column 6 of table6-12.xvg. The main reason why VOTCA uses the C12 columns instead of the C6 columns is historically, but one doesn't need both as for coarse-grained interactions the distinction between C6 and C12 makes not much sense. Christoph > > Should I use lammps instead of GROMACS. > > Thanks > > -- > 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.
