2013/7/12 <[email protected]>: > > > 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? This is not my field of expertise, so I will leave the question to somebody 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. > > -- 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.
