On Thursday, April 12, 2018 at 8:14:42 AM UTC-4, Christoph Junghans wrote: > > On Thu, Apr 12, 2018 at 3:39 AM, Alexander Alexander > <alexand...@gmail.com <javascript:>> wrote: > > > > Hi, > > > > I was wondering if it is normal to have table_b1,2,3,4.xvg like the > attached > > figures? They are the result if BI (similar script as hexane example) > over a > > 500 ns nvt simulation of a single molecule. What could be the meaning of > the > > straight line passing from point (0,0) in table_b1.xvg for example? > No they don't look normal, bonded interaction should always look like > an modified U with both sides, left and right, going to infinity. > I do not know what exactly I am doing wrong; I guess the 500 ns NVT simulation is fine to get statistic for a single molecule, and then I am following these command in the hexane example for to obtain bonded.xvg potential using BI:
#!/bin/bash -e #calculate bonded potentials with csg_boltzmann csg_boltzmann --top prdnvt.tpr --trj prdnvt.trr --cg mapp.xml --begin 2000 < boltzmann_cmds #smooth bonded potentials csg_call --sloppy-tables table smooth bond-LG-H1.pot.ib input_bond-LG-H1.pot csg_call --sloppy-tables table smooth bond-H1-H2.pot.ib input_bond-H1-H2.pot csg_call --sloppy-tables table smooth bond-H2-L.pot.ib input_bond-H2-L.pot csg_call --sloppy-tables table smooth bond-L-RG.pot.ib input_bond-L-RG.pot csg_call --sloppy-tables table smooth angle-LG-H1-H2.pot.ib input_angle-LG-H1-H2.pot csg_call --sloppy-tables table smooth angle-H1-H2-L.pot.ib input_angle-H1-H2-L.pot csg_call --sloppy-tables table smooth angle-H2-L-RG.pot.ib input_angle-H2-L-RG.pot csg_call --sloppy-tables table smooth dihedral-LG-H1-H2-L.pot.ib input_dihedral-LG-H1-H2-L.pot csg_call --sloppy-tables table smooth dihedral-H1-H2-L-RG.pot.ib input_dihedral-H1-H2-L-RG.pot #convert bonded potentials to GROMACS tables if [ -d table ]; then rm -r table fi mkdir table csg_call --ia-type bond --ia-name bond-LG-H1 --options bond-LG-H1.xml convert_potential gromacs --clean input_bond-LG-H1.pot table/table_b1.xvg csg_call --ia-type bond --ia-name bond-H1-H2 --options bond-H1-H2.xml convert_potential gromacs --clean input_bond-H1-H2.pot table/table_b2.xvg csg_call --ia-type bond --ia-name bond-H2-L --options bond-H2-L.xml convert_potential gromacs --clean input_bond-H2-L.pot table/table_b3.xvg csg_call --ia-type bond --ia-name bond-L-RG --options bond-L-RG.xml convert_potential gromacs --clean input_bond-L-RG.pot table/table_b4.xvg csg_call --ia-type angle --ia-name angle-LG-H1-H2 --options angle-LG-H1-H2.xml convert_potential gromacs --clean input_angle-LG-H1-H2.pot table/table_a1.xvg csg_call --ia-type angle --ia-name angle-H1-H2-L --options angle-H1-H2-L.xml convert_potential gromacs --clean input_angle-H1-H2-L.pot table/table_a2.xvg csg_call --ia-type angle --ia-name angle-H2-L-RG --options angle-H2-L-RG.xml convert_potential gromacs --clean input_angle-H2-L-RG.pot table/table_a3.xvg csg_call --ia-type angle --ia-name dihedral-LG-H1-H2-L --options dihedral-LG-H1-H2-L.xml convert_potential gromacs --clean input_dihedral-LG-H1-H2-L.pot table/table_d1.xvg csg_call --ia-type angle --ia-name dihedral-H1-H2-L-RG --options dihedral-H1-H2-L-RG.xml convert_potential gromacs --clean input_dihedral-H1-H2-L-RG.pot table/table_d2.xvg Even I have similar problem for a molecule with three beads. Attachment is a log.txt file out of running the above script. Any help would be highly appreciated. BTW, how the form of the angle-bonded potential should look like? The table_a1.xvg for hexane does not go to +infinity from the right leg. Thank you. Regards, Alex > > Also, is the format of the table_bonded.xvg is "x y [error bar]"? > x,y, force - see the gromacs manual for details. > > Christoph > > > Thank you. > > Regards, > > Alex > > > > On Wednesday, April 11, 2018 at 3:44:30 PM UTC-4, Christoph Junghans > wrote: > >> > >> On Wed, Apr 11, 2018 at 12:49 PM, Alexander Alexander > >> <alexand...@gmail.com> wrote: > >> > > >> > Hi Christoph, > >> > > >> > On Wednesday, April 11, 2018 at 8:22:24 AM UTC-4, Christoph Junghans > >> > wrote: > >> >> > >> >> > >> >> > >> >> On Wed, Apr 11, 2018, 01:51 Alexander Alexander < > alexand...@gmail.com> > >> >> wrote: > >> >>> > >> >>> > >> >>> Hi, > >> >>> You mean BI over a single molecule in vacuum? > >> >> > >> >> > >> >> Yes, or any potential, which has right equilibrium length/value. > >> > > >> > I decided to the BI for bonded interaction, the procedure and results > >> > for > >> > one of the molecule is shared in the below link, I am not sure if > >> > everything > >> > is fine, I would be so appreciated if you could kindly have a look > and > >> > give > >> > any suggestion, please. > >> > > >> > https://drive.google.com/open?id=1hvIH9mk1LfYo5LOO1VjBAkBZx7L0q3P0 > >> > > >> > Also, do the settings used in the hexane or spce water example in the > >> > tutorial are the real settings and parameters used in your > publication? > >> > or > >> > these are just examples. > >> Most of them are, but some got adapted a bit to be more instructive as > >> tutorials. > >> > >> Christoph > >> > > >> > Thanks. > >> > Regards, > >> > Alex > >> >> > >> >> > >> >>> > >> >>> Instead of sd integrater can md integrator (but still in NVT > ensemble) > >> >>> be > >> >>> used in IBI ( bonded and nonbonded or either of them) and still > have > >> >>> good > >> >>> results? > >> >> > >> >> > >> >> Sure as long as you are still sampling NVT you can use any > integrator. > >> >> However, usually sd is the more stable integrator, so I don't think > >> >> that > >> >> change will help with your problem. > >> >> > >> >> Christoph > >> >> > >> >>> Thanks, > >> >>> Alex > >> >>> > >> >>> -- > >> >>> 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 votca+un...@googlegroups.com. > >> >>> To post to this group, send email to vo...@googlegroups.com. > >> >>> 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 votca+un...@googlegroups.com. > >> > To post to this group, send email to vo...@googlegroups.com. > >> > 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 votca+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
alex@pc120 ~/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol▌▌▌./run_Boltzmann.sh Reading file prd-new.tpr, VERSION 2018 (single precision) I have 45 beads in 1 molecules I have 5 beads in 1 molecules for the coarsegraining trr version: GMX_trn_file (single precision) Interactive mode, expecting commands: help: show this help q: quit list: list all available bonds vals <file> <selection>: write values to file hist <file> <selection>: create histogram tab <file> <selection>: create tabulated potential autocor <file> <selection>: calculate autocorrelation, only one row allowed in selection! cor <file> <selection>: calculate correlations, first row is correlated with all other rows > > > > > > > > histogram created using 1 data-rows, written to > > > > > > > > bond-LG-H1.pot.ib > > > > > > > > histogram created using 1 data-rows, written to > > > > > > > > bond-H1-H2.pot.ib > > > > > > > > histogram created using 1 data-rows, written to bond-H2-L.pot.ib > > > > > > > > histogram created using 1 data-rows, written to bond-L-RG.pot.ib > > > > > > histogram created using 1 data-rows, written to > > > > > > angle-LG-H1-H2.pot.ib > > > > > > histogram created using 1 data-rows, written to angle-H1-H2-L.pot.ib > > > > > > histogram created using 1 data-rows, written to angle-H2-L-RG.pot.ib > > > > > > histogram created using 1 data-rows, written to > > > > > > dihedral-LG-H1-H2-L.pot.ib > > > > > > histogram created using 1 data-rows, written to > > > > > > dihedral-H1-H2-L-RG.pot.ib > > Running subscript 'table_smooth.pl bond-LG-H1.pot.ib input_bond-LG-H1.pot' > > (from tags table smooth) dir > > /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl bond-H1-H2.pot.ib input_bond-H1-H2.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl bond-H2-L.pot.ib input_bond-H2-L.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl bond-L-RG.pot.ib input_bond-L-RG.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl angle-LG-H1-H2.pot.ib input_angle-LG-H1-H2.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl angle-H1-H2-L.pot.ib input_angle-H1-H2-L.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl angle-H2-L-RG.pot.ib input_angle-H2-L-RG.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl dihedral-LG-H1-H2-L.pot.ib input_dihedral-LG-H1-H2-L.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_smooth.pl dihedral-H1-H2-L-RG.pot.ib input_dihedral-H1-H2-L-RG.pot' (from tags table smooth) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in bond-LG-H1.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-LG-H1.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in bond-LG-H1.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in bond-LG-H1.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-LG-H1.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_bond-LG-H1.pot table/table_b1.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_bond-LG-H1.pot to table/table_b1.xvg Running critical command 'mktemp input_bond-LG-H1.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_bond-LG-H1.pot --out input_bond-LG-H1.pot.smooth.zRZ0r --grid 0:0.001:0.4' Running critical command 'mktemp input_bond-LG-H1.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type bond input_bond-LG-H1.pot.smooth.zRZ0r input_bond-LG-H1.pot.extrapol.9ckdU' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_bond-LG-H1.pot.smooth.zRZ0r to input_bond-LG-H1.pot.extrapol.9ckdU Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_bond-LG-H1.pot.smooth.zRZ0r input_bond-LG-H1.pot.extrapol.9ckdU' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient 480.897393333337 table_extrapolate.pl: extrapolating the right using linear with gradient 0 Running critical command 'mktemp input_bond-LG-H1.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_bond-LG-H1.pot.extrapol.9ckdU --out input_bond-LG-H1.pot.interpol.3JERN --grid 0:0.001:0.4 --comment Created on Thu Apr 12 11:22:24 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/bond-LG-H1.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_bond-LG-H1.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type bond input_bond-LG-H1.pot.interpol.3JERN input_bond-LG-H1.pot.shift.aanLx' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type bond input_bond-LG-H1.pot.shift.aanLx table/table_b1.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in bond-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in bond-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in bond-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_bond-H1-H2.pot table/table_b2.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_bond-H1-H2.pot to table/table_b2.xvg Running critical command 'mktemp input_bond-H1-H2.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_bond-H1-H2.pot --out input_bond-H1-H2.pot.smooth.dBmTT --grid 0:0.001:0.5' Running critical command 'mktemp input_bond-H1-H2.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type bond input_bond-H1-H2.pot.smooth.dBmTT input_bond-H1-H2.pot.extrapol.2nZDK' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_bond-H1-H2.pot.smooth.dBmTT to input_bond-H1-H2.pot.extrapol.2nZDK Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_bond-H1-H2.pot.smooth.dBmTT input_bond-H1-H2.pot.extrapol.2nZDK' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient 508.6296 table_extrapolate.pl: extrapolating the right using linear with gradient 0 Running critical command 'mktemp input_bond-H1-H2.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_bond-H1-H2.pot.extrapol.2nZDK --out input_bond-H1-H2.pot.interpol.yYLVf --grid 0:0.001:0.5 --comment Created on Thu Apr 12 11:22:24 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/bond-H1-H2.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_bond-H1-H2.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type bond input_bond-H1-H2.pot.interpol.yYLVf input_bond-H1-H2.pot.shift.0pOym' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type bond input_bond-H1-H2.pot.shift.0pOym table/table_b2.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in bond-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in bond-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in bond-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_bond-H2-L.pot table/table_b3.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_bond-H2-L.pot to table/table_b3.xvg Running critical command 'mktemp input_bond-H2-L.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_bond-H2-L.pot --out input_bond-H2-L.pot.smooth.fyZtX --grid 0:0.001:4' Running critical command 'mktemp input_bond-H2-L.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type bond input_bond-H2-L.pot.smooth.fyZtX input_bond-H2-L.pot.extrapol.3Fx7Y' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_bond-H2-L.pot.smooth.fyZtX to input_bond-H2-L.pot.extrapol.3Fx7Y Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_bond-H2-L.pot.smooth.fyZtX input_bond-H2-L.pot.extrapol.3Fx7Y' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient 0 table_extrapolate.pl: extrapolating the right using linear with gradient 467.788469999999 Running critical command 'mktemp input_bond-H2-L.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_bond-H2-L.pot.extrapol.3Fx7Y --out input_bond-H2-L.pot.interpol.SJ0JC --grid 0:0.001:4 --comment Created on Thu Apr 12 11:22:25 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/bond-H2-L.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_bond-H2-L.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type bond input_bond-H2-L.pot.interpol.SJ0JC input_bond-H2-L.pot.shift.XcGqG' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type bond input_bond-H2-L.pot.shift.XcGqG table/table_b3.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in bond-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in bond-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in bond-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in bond-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_bond-L-RG.pot table/table_b4.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_bond-L-RG.pot to table/table_b4.xvg Running critical command 'mktemp input_bond-L-RG.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_bond-L-RG.pot --out input_bond-L-RG.pot.smooth.8eROj --grid 0:0.01:4' Running critical command 'mktemp input_bond-L-RG.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type bond input_bond-L-RG.pot.smooth.8eROj input_bond-L-RG.pot.extrapol.VWDYd' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_bond-L-RG.pot.smooth.8eROj to input_bond-L-RG.pot.extrapol.VWDYd Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_bond-L-RG.pot.smooth.8eROj input_bond-L-RG.pot.extrapol.VWDYd' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient -282.223722333333 table_extrapolate.pl: extrapolating the right using linear with gradient 0 Running critical command 'mktemp input_bond-L-RG.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_bond-L-RG.pot.extrapol.VWDYd --out input_bond-L-RG.pot.interpol.28IAS --grid 0:0.001:4 --comment Created on Thu Apr 12 11:22:25 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/bond-L-RG.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_bond-L-RG.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type bond input_bond-L-RG.pot.interpol.28IAS input_bond-L-RG.pot.shift.BlL4v' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type bond input_bond-L-RG.pot.shift.BlL4v table/table_b4.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in angle-LG-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in angle-LG-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in angle-LG-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in angle-LG-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in angle-LG-H1-H2.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_angle-LG-H1-H2.pot table/table_a1.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_angle-LG-H1-H2.pot to table/table_a1.xvg Running critical command 'mktemp input_angle-LG-H1-H2.pot.scale.XXXXX' Running subscript 'table_linearop.pl --on-x input_angle-LG-H1-H2.pot input_angle-LG-H1-H2.pot.scale.vUheT 57.2957795 0' (from tags table linearop) dir /home/alex/local/votca/share/votca/scripts/inverse table_linearop.pl: input_angle-LG-H1-H2.pot to input_angle-LG-H1-H2.pot.scale.vUheT with x' = 57.2957795*x + 0 Running critical command 'mktemp input_angle-LG-H1-H2.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_angle-LG-H1-H2.pot.scale.vUheT --out input_angle-LG-H1-H2.pot.smooth.g7HSn --grid 0:2.86479:180' Running critical command 'mktemp input_angle-LG-H1-H2.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type angle input_angle-LG-H1-H2.pot.smooth.g7HSn input_angle-LG-H1-H2.pot.extrapol.7q9Li' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_angle-LG-H1-H2.pot.smooth.g7HSn to input_angle-LG-H1-H2.pot.extrapol.7q9Li Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_angle-LG-H1-H2.pot.smooth.g7HSn input_angle-LG-H1-H2.pot.extrapol.7q9Li' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient 0 table_extrapolate.pl: extrapolating the right using linear with gradient -0.00784086093570557 Running critical command 'mktemp input_angle-LG-H1-H2.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_angle-LG-H1-H2.pot.extrapol.7q9Li --out input_angle-LG-H1-H2.pot.interpol.5RkKp --grid 0:0.001:180 --comment Created on Thu Apr 12 11:22:25 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/angle-LG-H1-H2.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_angle-LG-H1-H2.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type angle input_angle-LG-H1-H2.pot.interpol.5RkKp input_angle-LG-H1-H2.pot.shift.mCdiU' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type angle input_angle-LG-H1-H2.pot.shift.mCdiU table/table_a1.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in angle-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in angle-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in angle-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in angle-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in angle-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_angle-H1-H2-L.pot table/table_a2.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_angle-H1-H2-L.pot to table/table_a2.xvg Running critical command 'mktemp input_angle-H1-H2-L.pot.scale.XXXXX' Running subscript 'table_linearop.pl --on-x input_angle-H1-H2-L.pot input_angle-H1-H2-L.pot.scale.TbtEU 57.2957795 0' (from tags table linearop) dir /home/alex/local/votca/share/votca/scripts/inverse table_linearop.pl: input_angle-H1-H2-L.pot to input_angle-H1-H2-L.pot.scale.TbtEU with x' = 57.2957795*x + 0 Running critical command 'mktemp input_angle-H1-H2-L.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_angle-H1-H2-L.pot.scale.TbtEU --out input_angle-H1-H2-L.pot.smooth.V0WJ0 --grid 0:2.86479:180' Running critical command 'mktemp input_angle-H1-H2-L.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type angle input_angle-H1-H2-L.pot.smooth.V0WJ0 input_angle-H1-H2-L.pot.extrapol.4b4dl' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_angle-H1-H2-L.pot.smooth.V0WJ0 to input_angle-H1-H2-L.pot.extrapol.4b4dl Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_angle-H1-H2-L.pot.smooth.V0WJ0 input_angle-H1-H2-L.pot.extrapol.4b4dl' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient -0.383513846855558 table_extrapolate.pl: extrapolating the right using linear with gradient 0.178364654070048 Running critical command 'mktemp input_angle-H1-H2-L.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_angle-H1-H2-L.pot.extrapol.4b4dl --out input_angle-H1-H2-L.pot.interpol.2N03z --grid 0:0.001:180 --comment Created on Thu Apr 12 11:22:28 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/angle-H1-H2-L.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_angle-H1-H2-L.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type angle input_angle-H1-H2-L.pot.interpol.2N03z input_angle-H1-H2-L.pot.shift.pCu5T' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type angle input_angle-H1-H2-L.pot.shift.pCu5T table/table_a2.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in angle-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in angle-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in angle-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in angle-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in angle-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_angle-H2-L-RG.pot table/table_a3.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_angle-H2-L-RG.pot to table/table_a3.xvg Running critical command 'mktemp input_angle-H2-L-RG.pot.scale.XXXXX' Running subscript 'table_linearop.pl --on-x input_angle-H2-L-RG.pot input_angle-H2-L-RG.pot.scale.M7Bra 57.2957795 0' (from tags table linearop) dir /home/alex/local/votca/share/votca/scripts/inverse table_linearop.pl: input_angle-H2-L-RG.pot to input_angle-H2-L-RG.pot.scale.M7Bra with x' = 57.2957795*x + 0 Running critical command 'mktemp input_angle-H2-L-RG.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_angle-H2-L-RG.pot.scale.M7Bra --out input_angle-H2-L-RG.pot.smooth.wNeH4 --grid 0:2.86479:180' Running critical command 'mktemp input_angle-H2-L-RG.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type angle input_angle-H2-L-RG.pot.smooth.wNeH4 input_angle-H2-L-RG.pot.extrapol.MT8R5' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_angle-H2-L-RG.pot.smooth.wNeH4 to input_angle-H2-L-RG.pot.extrapol.MT8R5 Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_angle-H2-L-RG.pot.smooth.wNeH4 input_angle-H2-L-RG.pot.extrapol.MT8R5' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient -1.082253995767 table_extrapolate.pl: extrapolating the right using linear with gradient 0.829598149718944 Running critical command 'mktemp input_angle-H2-L-RG.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_angle-H2-L-RG.pot.extrapol.MT8R5 --out input_angle-H2-L-RG.pot.interpol.lYxnI --grid 0:0.001:180 --comment Created on Thu Apr 12 11:22:31 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/angle-H2-L-RG.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_angle-H2-L-RG.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type angle input_angle-H2-L-RG.pot.interpol.lYxnI input_angle-H2-L-RG.pot.shift.gyDot' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type angle input_angle-H2-L-RG.pot.shift.gyDot table/table_a3.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in dihedral-LG-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in dihedral-LG-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in dihedral-LG-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in dihedral-LG-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in dihedral-LG-H1-H2-L.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_dihedral-LG-H1-H2-L.pot table/table_d1.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_dihedral-LG-H1-H2-L.pot to table/table_d1.xvg Running critical command 'mktemp input_dihedral-LG-H1-H2-L.pot.scale.XXXXX' Running subscript 'table_linearop.pl --on-x input_dihedral-LG-H1-H2-L.pot input_dihedral-LG-H1-H2-L.pot.scale.JxeLu 57.2957795 0' (from tags table linearop) dir /home/alex/local/votca/share/votca/scripts/inverse table_linearop.pl: input_dihedral-LG-H1-H2-L.pot to input_dihedral-LG-H1-H2-L.pot.scale.JxeLu with x' = 57.2957795*x + 0 Running critical command 'mktemp input_dihedral-LG-H1-H2-L.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_dihedral-LG-H1-H2-L.pot.scale.JxeLu --out input_dihedral-LG-H1-H2-L.pot.smooth.3J4x4 --grid -180:5.72958:180' Running critical command 'mktemp input_dihedral-LG-H1-H2-L.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type dihedral input_dihedral-LG-H1-H2-L.pot.smooth.3J4x4 input_dihedral-LG-H1-H2-L.pot.extrapol.ljwrl' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_dihedral-LG-H1-H2-L.pot.smooth.3J4x4 to input_dihedral-LG-H1-H2-L.pot.extrapol.ljwrl Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_dihedral-LG-H1-H2-L.pot.smooth.3J4x4 input_dihedral-LG-H1-H2-L.pot.extrapol.ljwrl' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient nan table_extrapolate.pl: extrapolating the right using linear with gradient nan Running critical command 'mktemp input_dihedral-LG-H1-H2-L.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_dihedral-LG-H1-H2-L.pot.extrapol.ljwrl --out input_dihedral-LG-H1-H2-L.pot.interpol.CvmIv --grid -180:0.001:180 --comment Created on Thu Apr 12 11:22:34 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/dihedral-LG-H1-H2-L.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_dihedral-LG-H1-H2-L.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type dihedral input_dihedral-LG-H1-H2-L.pot.interpol.CvmIv input_dihedral-LG-H1-H2-L.pot.shift.Jc10Z' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type dihedral input_dihedral-LG-H1-H2-L.pot.shift.Jc10Z table/table_d1.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.scriptpath' found in dihedral-H1-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in dihedral-H1-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' csg_get_property: No value for 'cg.inverse.program' found in dihedral-H1-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in dihedral-H1-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: No value for 'cg.inverse.program' found in dihedral-H1-H2-L-RG.xml, trying /home/alex/local/votca/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.program' from /home/alex/local/votca/share/votca/xml/csg_defaults.xml: gromacs csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' Running subscript 'potential_to_gromacs.sh --clean input_dihedral-H1-H2-L-RG.pot table/table_d2.xvg' (from tags convert_potential gromacs) dir /home/alex/local/votca/share/votca/scripts/inverse Convert input_dihedral-H1-H2-L-RG.pot to table/table_d2.xvg Running critical command 'mktemp input_dihedral-H1-H2-L-RG.pot.scale.XXXXX' Running subscript 'table_linearop.pl --on-x input_dihedral-H1-H2-L-RG.pot input_dihedral-H1-H2-L-RG.pot.scale.pXQ0x 57.2957795 0' (from tags table linearop) dir /home/alex/local/votca/share/votca/scripts/inverse table_linearop.pl: input_dihedral-H1-H2-L-RG.pot to input_dihedral-H1-H2-L-RG.pot.scale.pXQ0x with x' = 57.2957795*x + 0 Running critical command 'mktemp input_dihedral-H1-H2-L-RG.pot.smooth.XXXXX' Running critical command 'csg_resample --in input_dihedral-H1-H2-L-RG.pot.scale.pXQ0x --out input_dihedral-H1-H2-L-RG.pot.smooth.RgQqD --grid -180:5.72958:180' Running critical command 'mktemp input_dihedral-H1-H2-L-RG.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --clean --type dihedral input_dihedral-H1-H2-L-RG.pot.smooth.RgQqD input_dihedral-H1-H2-L-RG.pot.extrapol.Dv79c' (from tags potential extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse Extrapolate input_dihedral-H1-H2-L-RG.pot.smooth.RgQqD to input_dihedral-H1-H2-L-RG.pot.extrapol.Dv79c Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright input_dihedral-H1-H2-L-RG.pot.smooth.RgQqD input_dihedral-H1-H2-L-RG.pot.extrapol.Dv79c' (from tags table extrapolate) dir /home/alex/local/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient nan table_extrapolate.pl: extrapolating the right using linear with gradient nan Running critical command 'mktemp input_dihedral-H1-H2-L-RG.pot.interpol.XXXXX' Running critical command 'csg_resample --in input_dihedral-H1-H2-L-RG.pot.extrapol.Dv79c --out input_dihedral-H1-H2-L-RG.pot.interpol.773mI --grid -180:0.001:180 --comment Created on Thu Apr 12 11:22:39 EDT 2018 by alex@pc120 called from potential_to_gromacs.sh, version 1.4.1 gitid: 73f8ce57 settings file: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol/dihedral-H1-H2-L-RG.xml working directory: /home/alex/test/CG/dw/molecule/ATB/bonded/cg/csg-boltzman-single-mol' Running critical command 'mktemp input_dihedral-H1-H2-L-RG.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type dihedral input_dihedral-H1-H2-L-RG.pot.interpol.773mI input_dihedral-H1-H2-L-RG.pot.shift.CpNXv' (from tags potential shift) dir /home/alex/local/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1e8 --type dihedral input_dihedral-H1-H2-L-RG.pot.shift.CpNXv table/table_d2.xvg' (from tags convert_potential xvg) dir /home/alex/local/votca/share/votca/scripts/inverse
