I have a problem in installation when I'm going to install it at another computer. When I run the csg_inverse command and the ERROR "source_wrapper: Could not get any script from tags 'functions' 'lammps' " occurs. I'm sure that I have installed lammps in this computer. So what's the proplem?
在 2018年11月30日星期五 UTC+8下午11:24:33，Christoph Junghans写道： > > > > On Fri, Nov 30, 2018 at 01:05 Lee <[email protected] <javascript:>> > wrote: > >> In votca, the smoothing process works for potential. Is there any >> smoothing process for new distribution? And what's the command? >> > No, but it would be hard to add! > > Also increasing the bin size naturally does smoothing! > > Christoph > >> >> >> 在 2018年11月21日星期三 UTC+8下午9:03:19，Christoph Junghans写道： >> >>> On Tue, Nov 20, 2018 at 6:44 PM Lee <[email protected]> wrote: >>> > >>> > The expression of boltzmann inversion is V=-kBTln(P). And the >>> distribution P is related to the scale of the x-coordinate. The plot of >>> bond distribution with different units are attached. In votca, all the >>> processes including calculating distributions and boltzmann inversion are >>> finished with units nm. So can I say that the obtained potential table used >>> in lammps is converted by V=-kBTln(P) with the length units nm? So in >>> lammps, the dynamic simulation is finished with length units angstroms but >>> with the potential corresponding to units nm. >>> >>> Well, V(x)= -kBTln(P(x)) and x can be a distance or an angle etc. V >>> and P are always parameterized by the same variable in its units. Also >>> P(x) is a distribution and hence is unit-less, plus the normalization >>> of the distribution doesn't matter much as ln(a*P)=ln a + ln P and >>> hence only leads to an irrelevant offset in the potential and doesn't >>> matter to the forces. >>> >>> Christoph >>> >>> > >>> > 在 2018年11月20日星期二 UTC+8下午11:43:59，Christoph Junghans写道： >>> >> >>> >> On Tue, Nov 20, 2018 at 2:04 AM Lee <[email protected]> wrote: >>> >> > >>> >> > I have another question. If my units command is real in lammps >>> which the units of distance and energy are angstroms and Kcal/mole >>> respectively, what shoud I change in the setting file in order to get the >>> potential table with right units? Now, the bond and angle potential of the >>> CG system are much lower than the corresponding atomic system. >>> >> >>> >> Usually VOTCA calculated things in Gromacs units (so nm, kJ/mol >>> etc.), >>> >> but if you only calculate RDFs you don't need to change anything as >>> >> input and output are both in nm and hence there is no scaling >>> >> involved. So this will work for angstroms as well. Additionally, you >>> >> need to make sure that kBT is in the right unit in the settings file. >>> >> >>> >> Christoph >>> >> > Thanks a lot. >>> >> > >>> >> > 在 2018年11月20日星期二 UTC+8上午5:52:29，Christoph Junghans写道： >>> >> >> >>> >> >> On Mon, Nov 19, 2018 at 8:51 AM Christoph Junghans < >>> [email protected]> wrote: >>> >> >> > >>> >> >> > On Sun, Nov 18, 2018 at 8:31 PM Lee <[email protected]> >>> wrote: >>> >> >> > > >>> >> >> > > For the dynamic simulations finished with lammps, should I set >>> the exclusions? If excluding non-bonded interactions between atoms that are >>> no further than 3 bonds away, does it need to excluding these atoms when >>> statistical target rdf distributon? >>> >> >> > > >>> >> >> > Yes, for LAMMPS you will most likely need to create rdf >>> exclusion manually. >>> >> >> > >>> >> >> > You can check, what exclusion VOTCA see by running: >>> >> >> > $ csg_dump --top <your_topology_file> --excl >>> >> >> > >>> >> >> > For advanced topology handling see, section 3.3 of the manual, >>> >> >> > http://doc.votca.org/manual.pdf >>> >> >> Also Joshua might be able to say something about the new LAMMPS >>> >> >> topology reader in csg and how exclusions are incorporated there. >>> >> >> >>> >> >> Christoph >>> >> >> > >>> >> >> > Christoph >>> >> >> > > -- >>> >> >> > > 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 https://groups.google.com/group/votca. >>> >> >> > > For more options, visit https://groups.google.com/d/optout. >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > -- >>> >> >> > Christoph Junghans >>> >> >> > Web: http://www.compphys.de >>> >> >> >>> >> >> >>> >> >> >>> >> >> -- >>> >> >> 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 https://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 https://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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> Visit this group at https://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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
