If a want to start a new simulation with box length say {30 30 30} and I need the coordinates from a previous simulations via: $last_configuration.gz" {time box_l npt_p_diff } {id pos type v f molecule}. The coordinates in this file (last_configuration.gz) are outside of the box size 30 30 30 because of they are unfolded. So, how ESPResSo treats these coordinates in my new box simulation [30 30 30]?
Thanks a lot for your time,
Salvador
----- Original Message ----- From: Axel Arnold <address@hidden> Date: Friday, April 9, 2010 3:15 am Subject: Re: [ESPResSo] Restarting a Simulation To: address@hidden
> On Thursday 08 April 2010 22:05:43 Salvador Herrera Velarde wrote: > > Hi All, > > > > First of all, thanks to ALL users and developers for your time > and help > > with all my questions. > > > > I using mbtools to run a simulation which contains a > large chain of > > monomers among other molecules. > > > > I want to restart the simulation with different conditions; to > save the > > actual configuration I was using the command: polyBlockWrite > > "$outputdir/$ident.[format %04d $j].gz" {time box_l npt_p_diff > } {id pos > > type v f molecule} > > > > Then, I used the generated file to restart the simulation. > However, when I > > visualized the snapshots in VMD, there are many bonds spanning > along the > > box simulation. I think this is an effect of the periodic boundary > > conditions. To fix the problem I tried to fold the positions: > > polyBlockWrite "$outputdir/$ident.[format %04d $j].gz" {time box_l > > npt_p_diff } {id folded_position type v f molecule} > > > > But still the same problem. > > > > Does anybody has an idea of how to fix the problem? > > First of all, for almost all purposes it is better to save the > unfolded > position in your blockfiles, since for example mean square > displacements are > otherwise incorrectly sampled after restarting. So, the first > version is the > way you want to save your data. > > Regarding the spanning bonds - that has nothing to do how > Espresso internally > stores the coordinates, therefore you get exactly the same > output whether you > use folded or positions in your blockfiles. This is indeed just > a problem of > visualization. Due to the periodic boundary conditions, you > always will have > bonds spanning the whole box when drawn nonperiodic. So, what > you would need > is a way to dynamically hide bonds which are longer than a > certain length, but > that VMD can't do as far as I know. Alternatively, if there is a > concept of > molecules in your setup, you can try to fold each of the > molecules > consistently according to its center of mass; look at Olaf's > pbctools how to > do that (http://www.espresso-pp.de/projects/pbctools). > > Cheers, > Axel > > > > -- > Dr. Axel Arnold Tel: +49 711 685 67609 > ICP, Universität Stuttgart Email: > address@hidden > Pfaffenwaldring 27 > 70569 Stuttgart, Germany > > > _______________________________________________ > ESPResSo mailing list > address@hidden > https://fias.uni-frankfurt.de/mailman/listinfo/espresso