Thank you anyway. I reduced cut-off in my mdp to 1 nm (from 3.5 nm) and the distributions look very similar (protein is not globular anymore) but still with values 1000 times bigger. Do you think decreasing the cutoff more would help?
Steven On Friday, July 12, 2013 4:31:22 PM UTC+1, Christoph Junghans wrote: > > 2013/7/12 <[email protected] <javascript:>>: > > > > > > 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] <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.
