Hi Sikandar: You are right. I made some mistakes about the parameters for potential conversion to espresso potential tables. It is working now based on youre suggestion. Thank you very much! Best Wishes! Zhicheng
2013/11/13 Sikandar Mashayak <[email protected]> > Hi > > I am sorry I was not clear in my response. > > The reason for the errors was that the table.xml file provided by you did > not contain all the required parameters for potential conversions to > espresso potential tables. Also, the sequence of parameters inside the > table.xml file was not right. > > I have corrected the table.xml file, which is attached below. May be you > can compare it with earlier settings to understand what was going wrong. > > I hope this helps. > > Cheers > Sikandar > > > On Thu, Nov 7, 2013 at 3:14 AM, 郭志成 <[email protected]> wrote: > >> Hi >> >> Thanks for your suggestion. For your comment, however, it is the method >> of calculating the coarse-grained potential using ibi procedure by espresso >> soft. I have obtained the coarse-grained potential (CG-CG.pot) calculated >> by gromacs with ibi procedure. I want to convert this potential to espresso >> format using csg_call convert_potential espresso. Anyway, thanks again for >> your reply. >> >> 2013/11/7 Chandan Choudhury <[email protected]> >> >>> >>> On Wed, Nov 6, 2013 at 9:32 PM, Sikandar Mashayak <[email protected] >>> > wrote: >>> >>>> Hi >>>> >>>> I am trying to reproduce the error, but when I run the same command >>>> 'csg_call --options table.xml --ia-type non-bonded --ia-name >>>> CG-CG convert_potential espresso CG-CG.pot tab', the command just get stuck >>>> and I am not getting any error or any kind of output. >>>> >>>> I am not sure why is csg_call getting stuck. >>>> >>> >>> Hi Sikandar, >>> >>> I second your observation. >>> This behavior is true for the 1.3-dev version. But if I try it on 1.2.3 >>> it executes. As I need to toggle between the two versions, this was never a >>> problem for for me. >>> >>> Chandan >>> >>>> >>>> Anyway, I guess, issue of property 'max' not found is due to incomplete >>>> information in table.xml. Try using the settings.xml given in ibi_esspresso >>>> tutorial instead of your table.xml. I hope that should work well. >>>> >>>> -- >>>> Sikandar >>>> >>>> >>>> On Wed, Nov 6, 2013 at 2:46 AM, Zhicheng <[email protected]> wrote: >>>> >>>>> Hi Christoph: >>>>> >>>>> Thanks for your reply. I use the 'csg_call --options table.xml >>>>> --ia-type non-bonded --ia-name CG-CG convert_potential espresso CG-CG.pot >>>>> tab' to convert the coarse-grained potential(CG-CG.pot) calculated by >>>>> gromacs ibi procedure to espresso format(tab). However, I get the >>>>> following >>>>> error message: >>>>> >>>>> >>>>> csg_get_interaction_property: Could not get 'max' for interaction with >>>>> name 'CG-CG' >>>>> from table.xml and no default was found in >>>>> >>>>> >>>>> /home/adminuser/votca_ctp/share/votca/xml/csg_defaults.xml Details can be >>>>> found above . >>>>> >>>>> >>>>> 在 2013年11月6日星期三UTC+8上午12时47分44秒，Christoph Junghans写道： >>>>> >>>>>> 2013/11/5 郭志成 <[email protected]>: >>>>>> > Hi: >>>>>> > >>>>>> > I convert the csg potential files to the tab format (as read by >>>>>> espresso) >>>>>> > using table_to_tab.pl (csg_call convert_potential tab). >>>>>> > >>>>>> > However, it needed three parameters (table_to_tab.sh in_pot >>>>>> in_deriv_pot >>>>>> > outfile). >>>>>> > >>>>>> > The problem is that I can not understand the meaning of >>>>>> in_deriv_pot. How >>>>>> > can I obtain the in_deriv_pot? >>>>>> csg_call convert_potential tab is just the low level script, which >>>>>> need an extra file with the derivatives in it. >>>>>> >>>>>> csg_call convert_potential espresso >>>>>> should do what you want to do. >>>>>> >>>>>> > >>>>>> > I will be very appreciable for any suggestion. >>>>>> > >>>>>> > -- >>>>>> > 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. >>>>> >>>> >>>> -- >>>> 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. >>>> >>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "votca" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/votca/ueau1mPHG_Q/unsubscribe. >>> To unsubscribe from this group and all its topics, 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. >>> >> >> -- >> 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. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/votca/ueau1mPHG_Q/unsubscribe. > To unsubscribe from this group and all its topics, 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. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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