2015-10-18 5:05 GMT-06:00 frank Zack <[email protected]>: > Hi all, > > Finally I've managed to use votca in combination with lammps and the results > are quite impressive. Any chances to the code you want to contribute?
> The only problem I could not solve is the pressure > correction. My naive approach is to equilibrate my parametrized coarse > grained polymer and then apply my target pressure for some steps. The final > configuration is then used again as input in ibi. This way I was able to get > quite close to the All-Atom-forcefield density. However, I guess the > pressure-correction-algorithm does a better job. The standard pressure correction never changes the density, but just adds an additional potential correction to change the pressure. > > Thats why i'm thinking about implementing the simple pressure correction > algorithm in conjunction with lammps as simulator. > From the documentation of votca it is not 100% clear how it works though. > What's the actual Input, the pressure correction needs? As far as i get it, > its just the average pressure of the latest md-run, right? > SO all I need is calculate the average pressure during my md-runs and the > rdf,right? > Which script-files do i have to edit (is it only postupd_pressure.sh) ? You will need to write a script like calc_pressure_gromacs.sh for LAMMPS. This calc_pressure_lammps.sh takes one argument - a filename, which contains one line "Pressure=XXX" after it got executed. See Section 9.1 of the manual to understand how to add a script in user space. Christoph > Thanks for any advice, > > regards, > frank. > > -- > 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/d/optout. -- 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/d/optout.
