Thanks! I'll try it and let you know how it works for me.
Best, Erez בתאריך יום חמישי, 9 בפברואר 2017 בשעה 04:59:59 UTC+2, מאת sikandar: > > Hi Erez, > > I have attached files to perform force-matching for spce water with lammps > trajectory. To run the exmaple, you will have to first run the lammps > simulation and generate the target trajectory. Then to perform force > matching run > > csg_fmatch --top topol.xml --traj traj.dump --cg water.xml --options > fmatch.xml > > I hope it helps. Let us know if you have any question. > > Best, > Sikandar > > On Wed, Feb 8, 2017 at 7:40 AM, Christoph Junghans <[email protected] > <javascript:>> wrote: > >> 2017-02-08 5:34 GMT-08:00 <[email protected] <javascript:>>: >> > Yes, insufficient disk space seems to be the problem. >> > >> > Another question: >> > Is it possible to perform force-matching using lammps dump files? >> Yes, if the dump file with the MD trajectory has forces csg_fmatch >> will read and use them: >> < >> https://github.com/votca/csg/blob/master/src/libcsg/modules/io/lammpsreader.cc#L218 >> > >> >> > I don't see a tutorial for this. >> I think Sikandar did that in the past and might be able to share some >> more details, but I think the only difference to the gromacs example >> is that you will need different trajectory and topology files. >> >> Christoph >> > If it is possible I'll appreciate any guidlines >> > >> > Thanks >> > Erez >> > >> > בתאריך יום שלישי, 7 בפברואר 2017 בשעה 16:32:43 UTC+2, מאת Christoph >> > Junghans: >> >> >> >> >> >> >> >> On Feb 7, 2017 01:28, <[email protected]> wrote: >> >> >> >> I removed the old VOTCA version and installed successfully the 1.5-dev >> >> version. >> >> Now the spce/ibi_lammps tutorial works; however at the 47th iteration >> the >> >> following error message appears: >> >> >> >> ERROR: >> >> critical: 'csg_stat --nt 4 --options >> >> /home/ereztamir/votca/bin/settings.xml --top topol.xml --trj traj.dump >> >> --begin 0 --first-frame 0' failed >> >> >> >> What is the meaning of this error? >> >> >> >> Attached is the inverse.log for more details >> >> >> >> The log says above the error message >> >> >> >> terminate called after throwing an instance of 'std::runtime_error' >> >> what(): Error: unexpected end of lammps file 'traj.dump' only 1133 >> >> atoms of 2180 read. >> >> >> >> So I guess the traj.dump of that step is corrupted! Did you ran out of >> >> disk space maybe? >> >> >> >> Christoph >> >> >> >> >> >> Thanks >> >> >> >> בתאריך יום שני, 6 בפברואר 2017 בשעה 17:45:45 UTC+2, מאת Christoph >> >> Junghans: >> >>> >> >>> >> >>> >> >>> On Feb 6, 2017 7:24 AM, <[email protected]> wrote: >> >>> >> >>> Hi Christoph, >> >>> Thank you for answering quickly. >> >>> .The VOTCA version is 1.2.4, seems like an old version. >> >>> >> >>> Yes, v1.2.4 is 2 years old. Currently is v1.4! >> >>> >> >>> This could be the problem? >> >>> How can I update it to the the current version? >> >>> >> >>> See here: >> >>> >> >>> https://github.com/votca/csg/wiki/Installing#from-source >> >>> >> >>> Christoph >> >>> >> >>> Thanks >> >>> Erez >> >>> >> >>> בתאריך יום שני, 6 בפברואר 2017 בשעה 16:13:58 UTC+2, מאת Christoph >> >>> Junghans: >> >>>> >> >>>> 2017-02-06 6:23 GMT-07:00 Erez Tamir <[email protected]>: >> >>>> > Dear votca usres, >> >>>> > >> >>>> > I'm trying to run votca-csg with LAMMPS, especially ibi_lammps >> >>>> > tutorial, and >> >>>> > always end with this error: >> >>>> > >> >>>> > ERROR: >> >>>> > source_wrapper: Could not get any script from tags 'functions' >> >>>> > 'lammps' >> >>>> > >> >>>> > I'm using Ubuntu 15.10 and lammps 15Mar2015 version. >> >>>> > First I installed votca using: sudo apt-get install votca-csg, >> updated >> >>>> > the >> >>>> > setting.xml file of the spce/ibi_lammps tutorial with the correct >> >>>> > lammps >> >>>> > command and run. This ended up with the above error. Then I >> searched a >> >>>> > solution in the votca forum and found a recommendation to install >> the >> >>>> > developmenet version, and so did (also installed all its >> dependencies) >> >>>> > via: >> >>>> > >> >>>> > < >> https://code.google.com/p/votca/wiki/Installing#Development_Version> >> >>>> We have moved to github, new information here: >> >>>> https://github.com/votca/csg/wiki/Installing#development-version >> >>>> >> >>>> > >> >>>> > Even after successful building of this votca vesion, the runs >> always >> >>>> > end >> >>>> > with the above error. >> >>>> > Would anyone help with this issue please? Should I update any >> other >> >>>> > file in >> >>>> > the tutorial? >> >>>> The Lammps tutorial should work with current version of VOTCA. >> >>>> >> >>>> Which version are you using? >> >>>> Run: >> >>>> $ csg_call --version >> >>>> >> >>>> Christoph >> >>>> > >> >>>> > Thanks, >> >>>> > Erez Tamir >> >>>> > IIT - Israel Institute of Technology >> >>>> > >> >>>> > -- >> >>>> > 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. >> >>> >> >>> >> >> -- >> >> 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. >> >> >> >> >> > -- >> > 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] <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. >> > > -- 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.
