Sure, I will have a look at it and let you know. Thanks Christoph.
On Wed, Jan 9, 2019 at 3:08 PM Christoph Junghans <[email protected]> wrote: > On Wed, Jan 9, 2019 at 8:36 AM Akash Banerjee <[email protected]> wrote: > > > > Thank you so much for your responses. I will do as you suggested. > Also if the problem stays reproducible, could you open an issue here: > https://github.com/votca/csg/issues and attach the input files. > > Christoph > > > > > Kind regards, > > Akash > > > > On Tue, Jan 8, 2019 at 7:56 PM Christoph Junghans <[email protected]> > wrote: > >> > >> On Tue, Jan 8, 2019 at 4:34 PM Akash Banerjee <[email protected]> > wrote: > >> > > >> > Hi Christoph, > >> > Thank you for your response. > >> > > >> > On Tue, Jan 8, 2019 at 2:30 PM Akash Banerjee <[email protected]> > wrote: > >> > > > >> > > Hi Christoph and other Votca developers, > >> > > > >> > > I am getting the errror- > >> > > > >> > > Error in `csg_stat': double free or corruption > >> > > > >> > > after 13 iterations. I understand that this error may occur due to > wrong naming. However, csg_stat managed to map my system for 13 iterations > and then went on to fail. > >> > > >> > Which version of VOTCA is this? Can you try the latest development > >> > version instead? > >> > > >> > I used the build.sh script on the website. The version is 1.5-dev > gitid: 648021c. I had recently built it on my cluster. Should I built is > again using the same build.sh command? > >> > > >> build.sh is obsolete, please use the new build system > >> ( > https://github.com/votca/votca/blob/master/share/doc/INSTALL.md#general-source-installation-instructions > ) > >> instead! We made some fixes in csg_stat recently, so you could try a > >> more recent version of csg if you want. > >> > >> > > >> > > Also, I have another questions, please have a look at your > convenience. > >> > > > >> > > I have run another system for 73 iterations and the values in > the bonded potential table (table_b1.xvg) is nearly the same as the 1st > iteration. I suspect that I am doing something wrong. > >> > > I have plotted the potential and attached it to this post with > the name potential_73th_iteration. I increased my simulation time for each > iteration from 100 ps to 1 ns. This change didnt make any > >> > > difference to the potentials. > >> > You need to zoom in around 0.5 to see any changes as the changes only > >> > happen around the minimum > >> > > >> > I got it. Should I be expecting negative values as a sign of > accuracy? (I am picturing a Lenard Jones Plot with a well depth) > >> Well, VOTCA shifts the potential, so that the minimum is at zero. So > >> you will have to determine the delta from a local maximum or so. > >> > >> Christoph > >> > > >> > Thank you again for your responses. > >> > > >> > On Tue, Jan 8, 2019 at 6:20 PM Christoph Junghans <[email protected]> > wrote: > >> >> > >> >> On Tue, Jan 8, 2019 at 2:30 PM Akash Banerjee <[email protected]> > wrote: > >> >> > > >> >> > Hi Christoph and other Votca developers, > >> >> > > >> >> > I am getting the errror- > >> >> > > >> >> > Error in `csg_stat': double free or corruption > >> >> > > >> >> > after 13 iterations. I understand that this error may occur due to > wrong naming. However, csg_stat managed to map my system for 13 iterations > and then went on to fail. > >> >> > >> >> Which version of VOTCA is this? Can you try the latest development > >> >> version instead? > >> >> > > >> >> > Please help me on the above. > >> >> > > >> >> > Also, I have another questions, please have a look at your > convenience. > >> >> > > >> >> > I have run another system for 73 iterations and the values in > the bonded potential table (table_b1.xvg) is nearly the same as the 1st > iteration. I suspect that I am doing something wrong. > >> >> > I have plotted the potential and attached it to this post with > the name potential_73th_iteration. I increased my simulation time for each > iteration from 100 ps to 1 ns. This change didnt make any > >> >> > difference to the potentials. > >> >> You need to zoom in around 0.5 to see any changes as the changes only > >> >> happen around the minimum. > >> >> > >> >> Christoph > >> >> > >> >> > > >> >> > > >> >> > Thank you for your help! > >> >> > > >> >> > Kind regards, > >> >> > Akash > >> >> > > >> >> > > >> >> > -- > >> >> > 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. > >> > > >> > > >> > > >> > -- > >> > akash > >> > > >> > -- > >> > 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. > > > > > > > > -- > > akash > > > > -- > > 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. > -- akash -- 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.
