2013/8/22 <[email protected]>: > I saw a huge change when I moved the whole potential of 1kj/mol so above cut > off the potential goes to -1 kj/mol never reaching zero. My CG distributions > are very close to atomistic and stopped converging... they have the same > shape though. I moved one potential and got better results but manually it > can be a pain. That doesn't seem right! Maybe you have forgotten to disable Gromacs' dispersion (DispCorr), which adds in extra forces when the potential doesn't go to 0. Anyhow, constants shift of the potential should not change the thermodynamics!
>From the technical side you can easily write a custom postadd routine to shift your potential every step $ cp `csg_call --show postupd dummy` postupd_magic.sh edit postupd_magic.sh, change the line critical cp $1 $2 to do_external table linearop $1 $2 1 XX where XX is the shift. Then $ echo "postupd magic postupd_magic.sh" > csg_table Add "$PWD" under scriptdir in your settings.xml file. As we always shift the potentials in VOTCA you also have to overwrite the default post update routines. $ cp `csg_call --show post_update_single ibi` my_post_update_generic_single.sh edit my_post_update_generic.sh and remove shift from the for loop. $ echo "post_update_single ibi my_post_update_generic_single.sh" >> csg_table Good luck, Christoph > > Steven > > W dniu czwartek, 22 sierpnia 2013 16:30:07 UTC+1 użytkownik Christoph > Junghans napisał: >> >> 2013/8/22 <[email protected]>: >> > Dear Users, >> > >> > I have one of my potentials in table_B_B.xvg. I wish to move the whole >> > potential of 1 kj/mol down to see how will that affect other >> > distributions. >> > Which tool can I use to also have derivatives in the last column? >> What is the point for this exercise? I can tell you right now, it will >> have no effect. >> >> If you subtract 1 kj/mol from the potential, the forces will be same >> and hence the distributions as MD is purely force driven. >> >> Christoph >> > >> > 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]. 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.
