On Friday, July 12, 2013 7:26:51 PM UTC+1, Tristan Bereau wrote: > > 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 >
Do you think I need a lot of iterations then? Or shall play with the cut off more? Steven > On Fri, Jul 12, 2013 at 7:04 PM, <[email protected] <javascript:>> > 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] <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. > > > > > -- 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.
