On Friday, July 12, 2013 1:48:06 AM UTC+1, Christoph Junghans wrote: > > 2013/7/11 <[email protected] <javascript:>>: > > 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 > > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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.
