On Friday, July 12, 2013 8:39:24 AM UTC+1, [email protected] wrote: > > > > On Friday, July 12, 2013 1:48:06 AM UTC+1, Christoph Junghans wrote: >> >> 2013/7/11 <[email protected]>: >> > Dear Users, >> > >> > I am running IBI - My system involves 90 beads, protein chain. Each >> > iteration is 5 ns and I am running 50 of them - at the begining. What I >> see >> > is that the first RDF has 100 times higher maximum than the target RDF. >> In >> > the second iteration it has 50 time higher maximum... in the third one >> it >> > has 5000 higher. >> Have a look at the trajectory with vmd, it might be that your protein >> forms a globule and never opens up again. >> > > Yes, this is true! It forms a globule and stack in this conformation. That > means the interactions are is too attractive... Would you suggest something? > I was thinking about using fully repulsive between acidic residues and > basic residues? And maybe exclude 1-4 interactions or divide them by 2? > > Steven >
I have in my topology: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 1.0 1.0 I would turn off the 1-4 interactions so set op nrexcl to 4 and apply fully repulsive to acidic-acidic basic-basic. How about vdwradii.dat? Shall increase it as it is taken from default settings i guess. Would you try sth else? Steven > > >> >> > Is that normal to have such fluctuations? Or maybe I have wrong values >> of >> > kbT in my settings which is >> > >> > <!-- 300*0.00831451 gromacs units --> >> > <kBT>2.49435</kBT> >> The order seems ok. And VOTCA will cross-check it with the value in >> your mdp file. >> > >> > Please, advise. >> > >> > Steven >> > >> > -- >> > 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/groups/opt_out. >> > >> > >> >> >> >> -- >> 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/groups/opt_out.
