Re: [votca] could not fetch table-extension from grompp.mdp - IBI

2013/7/10 s.neuman...@gmail.com: Thank you! Shall remove distributions and replace in my mxl file target into name.pot.in ? Or shall I just add to the list of files in xml that are copied? The target rdf (distribution != potential) stays the same, why would you change that? VOTCA always looks

Re: [votca] could not fetch table-extension from grompp.mdp - IBI

2013/7/10 s.neuman...@gmail.com: W dniu środa, 10 lipca 2013 15:12:58 UTC+1 użytkownik Christoph Junghans napisał: 2013/7/10 s.neu...@gmail.com: Thank you! Shall remove distributions and replace in my mxl file target into name.pot.in ? Or shall I just add to the list of files in xml

Re: [votca] could not fetch table-extension from grompp.mdp - IBI

2013/7/10 s.neuman...@gmail.com: On Wednesday, July 10, 2013 7:00:16 PM UTC+1, s.neu...@gmail.com wrote: Thank you. I sorted it out. Sorry, I have another question: I am running IBI on the cluster so I specified in my PBS script 16 cpus. When I run gromacs I always add mpiexec before

Re: [votca] could not fetch table-extension from grompp.mdp - IBI

2013/7/9 s.neuman...@gmail.com: My file which potential is converted to zero: # This file was created Tue Jul 9 08:47:14 2013 # by the following command: # g_rdf -f C_300_2100ns_45K.xtc -s em.tpr -o ACI-ACI.dist.new -bin 0.02 -n index_RDF.ndx # # g_rdf is part of G R O M A C S: # #

Re: [votca] could not fetch table-extension from grompp.mdp - IBI

2013/7/9 s.neuman...@gmail.com: I tried increasing min, changed the maximum of potential and it still provides me with zero potentials... I cannot upgrade to 1.3 as I am not an administrator. You don't need admin rights to install VOTCA in your home, right? On Monday, July 8, 2013 10:26:41

Re: [votca] could not fetch table-extension from grompp.mdp - IBI

2013/7/9 s.neuman...@gmail.com: This is what fails and produces the zero potential: Running subscript 'RDF_to_POT.pl ACI-ACI.dist.tgt ACI-ACI.pot.new.raw.396'(from tags rdf pot) Use of uninitialized value in subtraction (-) at

Re: [votca] could not fetch table-extension from grompp.mdp - IBI

2013/7/8 s.neuman...@gmail.com: Dear Users, I am trying to run IBI. I have 5 type of beads: POL, NON, GLY, ACI, BAS My setting.xml: cg non-bonded nameACI-ACI/name type1ACI/type1 type2ACI/type2 !-- dimension + grid spacing of tables for calculations -- min0/min

Re: [votca] could not fetch table-extension from grompp.mdp - IBI

W dniu poniedziałek, 8 lipca 2013 14:39:49 UTC+1 użytkownik Christoph Junghans napisał: 2013/7/8 s.neu...@gmail.com javascript:: Dear Users, I am trying to run IBI. I have 5 type of beads: POL, NON, GLY, ACI, BAS My setting.xml: cg non-bonded nameACI-ACI/name