One question: what is in your system? Just one protein with water? If that's the case, you'll have a hard time getting a RDF (which calculates the deviation from an average density), since you don't have a pure-liquid of these beads.
Tristan On Fri, Jul 12, 2013 at 7:04 PM, <[email protected]> wrote: > 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]>: >> > >> > >> > 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. > > -- 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.
