2015-10-18 9:15 GMT-06:00 frank Zack <[email protected]>: > Hi Christoph, > > thx again for your support this great tool. Im glad I didnt give up. > Meanwhile I've tested my new cg-potential in a tensile test of 40 chains of > PP each having 2400 repeats units. The result is surprisignly close to the > experiment (simulation is still running) and i can use a timestep of 30 fs. > > I surley can share my little code-modifications. But its very sloppy and I > just built a little "workaround". However, I've appended the modified files > and if you replace the original scripts, votca will only work with lammps > and no pressure correction is implemented yet. So do a backup of those > files. > csg_stat is replaced by a simple bash script. The rdfs and distributions are > calculated within lammps as defined in the lammps-input-script. The > lammps-script calls another bash-script which converts the tables from > gromacs-units to units-real (see lammps doc:distance=Angstrom, > Energy=kcal/mole). This file has to be added into the <filelist> -section in > your settings.xml. The options for the histrograms need to be adjusted in > the lammps-input script. The values defined in settings.xml are ignored. > > Keep in mind: Im not a professional, this is only a little hack. Its not a > full implementation and im not a about to learn perl to do so. Its working > for me and maybe it will work for somebody else too.. Thanks for sharing you scripts!
I incorporated parts of it in VOTCA: <https://github.com/votca/csg/commit/fb9f982e27cc6ddc3285d46dbbbb262a0481ff4f> However, replacing csg_stat is no-go, mainly because csg_stat can calculate IMC correlation matrices, too and it is parallel. My guess is that once you have written a mapping file like the one generated by the script I attached csg_stat will work. In case of lammps, which has multiple unit system, we only support the native one, meaning we assume everything is in nm and that will work fine, because all the scaling is linear. E.g. VOTCA reads a LAMMPS trajectory in any units assuming it is nm and then calculates the potentials in nm, which are basically the original units. It only becomes problematic if you pdb or xyz files because these are defined to be in Angstrom and hence VOTCA scales them by 10. Christoph > > 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.
gen.sh
Description: Bourne shell script
