2015-11-18 14:56 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Votca Users, > > I am trying to do fmatch for the liquid epoxy polymers containing two > types of molecules, 1) Epoxy, 2) Jeffamine-D230 (curing agent). > > I successfully created trajectory file for 20ns using gromacs. The > atomistic topology files (top and tpr) were also created. > > What I have done is > 1) Run 20ns for the system(15000 atoms) > 2) copy fmatch.xml from the one from the csg_tutorials. > 3) Run -> csg_fmatch --top topol.tpr --trj traj.trr --begin 2000 --option > fmatch.xml --cg "DGA.xml;J230.xml" > > There are A and B types in the DGA.xml, C and D types in the J230.xml. > > I tested A-A, B-B, C-C, D-D in the fmatch.xml file separately. The following > is the example of A-A case. The CG-CG.force file was written but all values > are "nan". B-B, C-C, and D-D cases are the same as nan. I have tried to > reduce step and increase <frames_per_block> numbers but the results are > same. Would you give me any comments for fixing this situation? I visualized > the simulation trajectories (traj.trr). It seems nothing wrong with that. > > <cg> > <fmatch> > <constrainedLS>false</constrainedLS> > <frames_per_block>5</frames_per_block> > </fmatch> > > <!-- example for a non-bonded interaction entry --> > <non-bonded> > <!-- name of the interaction --> > <name>CG-CG</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>A</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0</min> > <max>1.54</max> > <step>0.01</step> > <fmatch> > <min>0.3</min> > <max>1.00</max> > <step>0.001</step> That seems tiny, try 0.01 or even 0.05.
Christoph > <out_step>0.0001</out_step> > </fmatch> > </non-bonded> > </cg> > > > Thank you very much for your comments. > > Best regards, > Changwoon Jang > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
