your pull force looks insanly high especially if your pulling a small piece of residue? But for a whole protein of averidge 40 KDa, or 350 amino acids its around 2000 to 3000 from liturature (only about 6 that I could find anyways). I might thus be wrong, but wounder if you have a pull rate and force what one wins?
Stephan -------- Original-Nachricht -------- > Datum: Thu, 12 Jul 2012 18:15:53 +0200 > Von: Thomas Schlesier <[email protected]> > An: [email protected] > Betreff: [gmx-users] Final state not reached in pulling simulation > It could be possible tht you do not pull into the 'right' direction. if > there is another group between 'GTP' and 'Residue' you will get clashes > and 'Residue' won't move further (could be a water molecule, or some > other part of 'GTP'). > If this happens you should observe an increase in the force due to the > umbrella potential. > If the problems are due to waters molecules which block the 'pathway' > you could just delete them. > If another group is in the way, you might want to change the pull-vector > (and if lucky find the right one). But don't know what would be the best > strategy in this case. Maybe you can look into what docking-people do, > seems to me that your simulation is related to what they do (but myself > has absolute no knowledge about docking simulations). > > greetings > thomas > > > > Am 12.07.2012 17:26, schrieb [email protected]: > > Hello all, > > > > I m performing a pulling simulation on my Protein-Mg-GTP complex. I > > have considered pulling between the GTP and a residue of protein. > > The pull code in the .mdp file im using is as follows: > > > > > > ; Pull code > > pull = umbrella > > pull_geometry = distance ; simple distance increase > > pull_dim = N N Y > > pull_start = yes ; define initial COM distance> 0 > > pull_ngroups = 1 > > pull_group0 = GTP > > pull_group1 = Residue > > pull_rate1 = -0.00005 ; 0.00005 nm per ps = .05 nm per ns > > pull_k1 = 10000 ; kJ mol^-1 nm^-2 > > > > > > > > The initial distance between GTP and the residue was 7 A and the > > desired one was 3A. After the completion of run (10ns), I could get a > > trajectory where the final distance was still 4.25 A. > > > > I tried to continue the simulation for another 10ns with the same > > value for pull_k1 parameter and one by increasing the value to 100,000 > > also. In both of the case, the trajectories showed the distance > > stabilized near _4.25 A only. > > Can anyone please tell me the reason behind it? What should I do, so > > that I could get the desired distance ? > > > > Any suggestion and help is welcome !!! > > > > > > Thanks, > > > > Neeru Sharma > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
