2013/7/10 <[email protected]>: > Please, see attached all 3 distributions which produce zero potentials as > well as my settings.xml file. All the rest 12 files produce reasonable > potentials. In case my topology and mdp file as well as index file. I got!
Did you even had a look at ACI-ACI.dist.tgt, BAS-BAS.dist.tgt and POL-BAS.dist.tgt? These don't look like normal non-bonded distributions, which go to 1 for large r. Instead they tend toward 0 for large r, more like bonded distributions. And this is the reason why VOTCA cannot calculate an initial potential from the rdfs, in RDF_to_POT.pl we make the assumption that right end of the distribution is always valid, which isn't the case for your setup. My advise for you is: - check these distributions again - you might need to give them to VOTCA as bonded distributions. VOTCA makes the assumption that non-bonded potential go to 0, for large r, which isn't the case for these. Marking them as bonded distributions might work as their shape is more bond like. - 15 rdf is really a brave proposal, you might first want to coarse-grain the intra-molecular interactions for a vacuum simulation. > > Steven > > W dniu wtorek, 9 lipca 2013 16:38:57 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 2013/7/9 <[email protected]>: >> > So the script prepare_generic_single.sh prepares empty potential. >> > Please, >> > see attached files >> I save BAS-BAS.dist.tgt as BAS-BAS.dist.new and run: >> $ csg_call --ia-type non-bonded --options settings.xml --ia-name >> BAS-BAS prepare_single ibi >> BAS-BAS.pot.new looks good. >> Then I run: >> $ csg_call --ia-type non-bonded --options settings.xml --ia-name >> BAS-BAS convert_potential gromacs BAS-BAS.pot.new table_BAS_BAS.xvg >> and table_BAS_BAS.xvg looks ok, too. >> >> Using VOTCA 1.2.3: >> $ csg_call --version >> csg_call, version 1.2.3 hgid: d8ff5b538018 >> >> There might be one problem in your settings.xml file! I would never >> ever name a target *.dist.new! >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>ACI-ACI.dist.new</target> >> This might conflict with the dist.new generated inside the IBI iteration. >> Try to rename your target *.dist.tgt or something. >> >> And try to clean up your working directory: >> $ csg_inverse --options settings.xml clean >> >> > >> > Steven >> > >> > >> > On Tuesday, July 9, 2013 9:20:49 AM UTC+1, [email protected] wrote: >> >> >> >> 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: >> >> # >> >> # GROwing Monsters And Cloning Shrimps >> >> # >> >> @ title "Radial distribution" >> >> @ xaxis label "r" >> >> @ yaxis label "" >> >> @TYPE xy >> >> @ subtitle "ACIDIC_r1 - ACIDIC_r2" >> >> 0 0 >> >> 0.02 0 >> >> 0.04 0 >> >> 0.06 0 >> >> 0.08 0 >> >> 0.1 0 >> >> 0.12 0 >> >> 0.14 0 >> >> 0.16 0 >> >> 0.18 0 >> >> 0.2 0 >> >> 0.22 0 >> >> 0.24 0 >> >> 0.26 0 >> >> 0.28 0 >> >> 0.3 0 >> >> 0.32 0 >> >> 0.34 0 >> >> 0.36 0 >> >> 0.38 0 >> >> 0.4 0 >> >> 0.42 0.428026 >> >> 0.44 2.73004 >> >> 0.46 3.56834 >> >> 0.48 7.86533 >> >> 0.5 10.2691 >> >> 0.52 8.93595 >> >> 0.54 8.28634 >> >> 0.56 16.8549 >> >> 0.58 25.1403 >> >> 0.6 31.8824 >> >> 0.62 43.6097 >> >> 0.64 45.1671 >> >> 0.66 39.6977 >> >> 0.68 34.2941 >> >> 0.7 39.4517 >> >> 0.72 47.0501 >> >> 0.74 60.2617 >> >> 0.76 83.1488 >> >> 0.78 90.1104 >> >> 0.8 86.841 >> >> 0.82 113.766 >> >> 0.84 124.038 >> >> 0.86 117.723 >> >> 0.88 122.185 >> >> 0.9 133.969 >> >> 0.92 138.468 >> >> 0.94 136.485 >> >> 0.96 126.105 >> >> 0.98 114.327 >> >> 1 104.815 >> >> 1.02 89.205 >> >> 1.04 82.5255 >> >> 1.06 67.4105 >> >> 1.08 63.1886 >> >> 1.1 58.2909 >> >> 1.12 55.5656 >> >> 1.14 51.483 >> >> 1.16 50.7894 >> >> 1.18 44.9605 >> >> 1.2 43.0024 >> >> 1.22 44.0899 >> >> 1.24 44.8404 >> >> 1.26 44.4271 >> >> 1.28 40.0075 >> >> 1.3 36.8646 >> >> 1.32 32.5488 >> >> 1.34 30.4067 >> >> 1.36 29.3558 >> >> 1.38 24.9819 >> >> 1.4 24.2348 >> >> 1.42 21.909 >> >> 1.44 20.1757 >> >> 1.46 20.8667 >> >> 1.48 18.6171 >> >> 1.5 16.9829 >> >> 1.52 14.5778 >> >> 1.54 13.1508 >> >> 1.56 11.0781 >> >> 1.58 9.98262 >> >> 1.6 9.0561 >> >> 1.62 7.22253 >> >> 1.64 6.7386 >> >> 1.66 7.04308 >> >> 1.68 6.20748 >> >> 1.7 6.27133 >> >> 1.72 5.7434 >> >> 1.74 5.23803 >> >> 1.76 4.68082 >> >> 1.78 4.60007 >> >> 1.8 4.21872 >> >> 1.82 3.26017 >> >> 1.84 3.54656 >> >> 1.86 2.77218 >> >> 1.88 3.33315 >> >> 1.9 3.91185 >> >> 1.92 3.33912 >> >> 1.94 3.1703 >> >> 1.96 3.00764 >> >> 1.98 3.10127 >> >> 2 2.8319 >> >> 2.02 2.29492 >> >> 2.04 1.88721 >> >> 2.06 1.95752 >> >> 2.08 1.25676 >> >> 2.1 1.54118 >> >> 2.12 1.2938 >> >> 2.14 1.10483 >> >> 2.16 0.712186 >> >> 2.18 0.413146 >> >> 2.2 0.171631 >> >> 2.22 0.168553 >> >> 2.24 0.105354 >> >> 2.26 0.0887123 >> >> 2.28 0.0145271 >> >> 2.3 0.0428265 >> >> 2.32 0.0701525 >> >> 2.34 0.124125 >> >> 2.36 0.108471 >> >> 2.38 0.173316 >> >> 2.4 0.131107 >> >> 2.42 0.154739 >> >> 2.44 0.190263 >> >> 2.46 0.162227 >> >> 2.48 0.184177 >> >> 2.5 0.108746 >> >> 2.52 0.166485 >> >> 2.54 0.175579 >> >> 2.56 0.241984 >> >> 2.58 0.249593 >> >> 2.6 0.245769 >> >> 2.62 0.132016 >> >> 2.64 0.108353 >> >> 2.66 0.138749 >> >> 2.68 0.063085 >> >> 2.7 0.0310773 >> >> 2.72 0.0408292 >> >> 2.74 0.0201177 >> >> 2.76 0.00991358 >> >> 2.78 0 >> >> 2.8 0.00963237 >> >> 2.82 0 >> >> 2.84 0 >> >> 2.86 0 >> >> 2.88 0 >> >> 2.9 0 >> >> 2.92 0 >> >> 2.94 0 >> >> 2.96 0 >> >> 2.98 0 >> >> 3 0 >> >> 3.02 0 >> >> 3.04 0 >> >> 3.06 0 >> >> 3.08 0 >> >> 3.1 0 >> >> 3.12 0 >> >> 3.14 0 >> >> 3.16 0 >> >> 3.18 0 >> >> 3.2 0 >> >> 3.22 0 >> >> 3.24 0 >> >> 3.26 0 >> >> 3.28 0 >> >> 3.3 0 >> >> 3.32 0 >> >> 3.34 0 >> >> 3.36 0 >> >> 3.38 0 >> >> 3.4 0 >> >> 3.42 0 >> >> 3.44 0 >> >> 3.46 0 >> >> 3.48 0 >> >> 3.5 0 >> >> 3.52 0 >> >> 3.54 0 >> >> 3.56 0 >> >> 3.58 0 >> >> 3.6 0 >> >> 3.62 0 >> >> 3.64 0 >> >> 3.66 0 >> >> 3.68 0 >> >> 3.7 0 >> >> 3.72 0 >> >> 3.74 0 >> >> 3.76 0 >> >> 3.78 0 >> >> 3.8 0 >> >> 3.82 0 >> >> 3.84 0 >> >> 3.86 0 >> >> 3.88 0 >> >> 3.9 0 >> >> 3.92 0 >> >> 3.94 0 >> >> 3.96 0 >> >> 3.98 0 >> >> 4 0 >> >> 4.02 0 >> >> 4.04 0 >> >> 4.06 0 >> >> 4.08 0 >> >> 4.1 0 >> >> 4.12 0 >> >> 4.14 0 >> >> 4.16 0 >> >> 4.18 0 >> >> 4.2 0 >> >> 4.22 0 >> >> 4.24 0 >> >> 4.26 0 >> >> 4.28 0 >> >> 4.3 0 >> >> 4.32 0 >> >> 4.34 0 >> >> 4.36 0 >> >> 4.38 0 >> >> 4.4 0 >> >> 4.42 0 >> >> 4.44 0 >> >> 4.46 0 >> >> 4.48 0 >> >> 4.5 0 >> >> 4.52 0 >> >> 4.54 0 >> >> 4.56 0 >> >> 4.58 0 >> >> 4.6 0 >> >> 4.62 0 >> >> 4.64 0 >> >> 4.66 0 >> >> 4.68 0 >> >> >> >> >> >> On Tuesday, July 9, 2013 9:01:59 AM UTC+1, [email protected] wrote: >> >>> >> >>> Thank you. >> >>> The problem I face is that in step 000 some potentials have zero >> >>> values. >> >>> Hence in step 001 Votca cannot extrapolate them. No clue why thoose >> >>> potentials are zero values though... >> >>> >> >>> On Monday, July 8, 2013 10:26:41 PM UTC+1, Christoph Junghans wrote: >> >>>> >> >>>> 2013/7/8 <[email protected]>: >> >>>> > >> >>>> > >> >>>> > W dniu poniedziałek, 8 lipca 2013 18:00:32 UTC+1 użytkownik >> >>>> > Christoph >> >>>> > Junghans napisał: >> >>>> >> >> >>>> >> 2013/7/8 <[email protected]>: >> >>>> >> > >> >>>> >> > >> >>>> >> > W dniu poniedziałek, 8 lipca 2013 16:44:20 UTC+1 użytkownik >> >>>> >> > Christoph >> >>>> >> > Junghans napisał: >> >>>> >> >> >> >>>> >> >> 2013/7/8 <[email protected]>: >> >>>> >> >> > >> >>>> >> >> > >> >>>> >> >> > W dniu poniedziałek, 8 lipca 2013 14:39:49 UTC+1 użytkownik >> >>>> >> >> > Christoph >> >>>> >> >> > Junghans napisał: >> >>>> >> >> >> >> >>>> >> >> >> 2013/7/8 <[email protected]>: >> >>>> >> >> >> > 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> >> >>>> >> >> >> > <name>ACI-ACI</name> >> >>>> >> >> >> > <type1>ACI</type1> >> >>>> >> >> >> > <type2>ACI</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>ACI-ACI.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_ACI_ACI.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>ACI-BAS</name> >> >>>> >> >> >> > <type1>ACI</type1> >> >>>> >> >> >> > <type2>BAS</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>ACI-BAS.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_ACI_BAS.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>ACI-GLY</name> >> >>>> >> >> >> > <type1>ACI</type1> >> >>>> >> >> >> > <type2>GLY</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>ACI-GLY.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_ACI_GLY.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>ACI-NON</name> >> >>>> >> >> >> > <type1>ACI</type1> >> >>>> >> >> >> > <type2>NON</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>ACI-NON.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_ACI_NON.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>ACI-POL</name> >> >>>> >> >> >> > <type1>ACI</type1> >> >>>> >> >> >> > <type2>POL</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>ACI-POL.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_ACI_POL.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>BAS-BAS</name> >> >>>> >> >> >> > <type1>BAS</type1> >> >>>> >> >> >> > <type2>BAS</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>BAS-BAS.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_BAS_BAS.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>BAS-GLY</name> >> >>>> >> >> >> > <type1>BAS</type1> >> >>>> >> >> >> > <type2>GLY</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>BAS-GLY.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_BAS_GLY.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>GLY-GLY</name> >> >>>> >> >> >> > <type1>GLY</type1> >> >>>> >> >> >> > <type2>GLY</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>GLY-GLY.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_GLY_GLY.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>GLY-NON</name> >> >>>> >> >> >> > <type1>GLY</type1> >> >>>> >> >> >> > <type2>NON</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>GLY-NON.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_GLY_NON.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>GLY-POL</name> >> >>>> >> >> >> > <type1>GLY</type1> >> >>>> >> >> >> > <type2>POL</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>GLY-POL.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_GLY_POL.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>NON-BAS</name> >> >>>> >> >> >> > <type1>NON</type1> >> >>>> >> >> >> > <type2>BAS</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>NON-BAS.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_NON_BAS.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>NON-NON</name> >> >>>> >> >> >> > <type1>NON</type1> >> >>>> >> >> >> > <type2>NON</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>NON-NON.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_NON_NON.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>POL-BAS</name> >> >>>> >> >> >> > <type1>POL</type1> >> >>>> >> >> >> > <type2>BAS</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>POL-BAS.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_POL_BAS.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>POL-NON</name> >> >>>> >> >> >> > <type1>POL</type1> >> >>>> >> >> >> > <type2>NON</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>POL-NON.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_POL_NON.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > <non-bonded> >> >>>> >> >> >> > <name>POL-POL</name> >> >>>> >> >> >> > <type1>POL</type1> >> >>>> >> >> >> > <type2>POL</type2> >> >>>> >> >> >> > <!-- dimension + grid spacing of tables for >> >>>> >> >> >> > calculations >> >>>> >> >> >> > --> >> >>>> >> >> >> > <min>0</min> >> >>>> >> >> >> > <max>2.0</max> >> >>>> >> >> >> > <step>0.01</step> >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <target>POL-BAS.dist.new</target> >> >>>> >> >> >> > <!-- update cycles --> >> >>>> >> >> >> > <do_potential>1</do_potential> >> >>>> >> >> >> > <post_update></post_update> >> >>>> >> >> >> > <post_add>convergence</post_add> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <table>table_POL_POL.xvg</table> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </non-bonded> >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > <inverse> >> >>>> >> >> >> > <!-- 300*0.00831451 gromacs units --> >> >>>> >> >> >> > <kBT>2.49435</kBT> >> >>>> >> >> >> > <program>gromacs</program> >> >>>> >> >> >> > <gromacs> >> >>>> >> >> >> > <equi_time>10</equi_time> >> >>>> >> >> >> > <table_bins>0.002</table_bins> >> >>>> >> >> >> > <pot_max>1000000</pot_max> >> >>>> >> >> >> > <table_end>3.0</table_end> >> >>>> >> >> >> > </gromacs> >> >>>> >> >> >> > <filelist>grompp.mdp topol.top table*xvg >> >>>> >> >> >> > index.ndx</filelist> >> >>>> >> >> >> > <iterations_max>500</iterations_max> >> >>>> >> >> >> > <convergence_check>default</convergence_check> >> >>>> >> >> >> > <convergence_check_options> >> >>>> >> >> >> > <limit>0.001</limit> >> >>>> >> >> >> > <name_glob>*.conv</name_glob> >> >>>> >> >> >> > </convergence_check_options> >> >>>> >> >> >> > <method>ibi</method> >> >>>> >> >> >> > <log_file>inverse.log</log_file> >> >>>> >> >> >> > <restart_file>restart_points.log</restart_file> >> >>>> >> >> >> > </inverse> >> >>>> >> >> >> > </cg> >> >>>> >> >> >> > >> >>>> >> >> >> > and my grompp.mdp >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > integrator = md >> >>>> >> >> >> > tinit = 0.0 >> >>>> >> >> >> > dt = 0.002 >> >>>> >> >> >> > nsteps = 25000000 ; 50 ns >> >>>> >> >> >> > nstcomm = 100 >> >>>> >> >> >> > nstcalcenergy = 100 >> >>>> >> >> >> > >> >>>> >> >> >> > nstxout = 0 >> >>>> >> >> >> > nstvout = 0 >> >>>> >> >> >> > nstenergy = 0 >> >>>> >> >> >> > nstlog = 10000 >> >>>> >> >> >> > nstxtcout = 100 >> >>>> >> >> >> > energygrps = ACI BAS GLY NON POL >> >>>> >> >> >> > energygrp_table = ACI ACI ACI BAS ACI GLY ACI NON >> >>>> >> >> >> > ACI POL >> >>>> >> >> >> > BAS >> >>>> >> >> >> > BAS >> >>>> >> >> >> > BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS >> >>>> >> >> >> > POL >> >>>> >> >> >> > NON >> >>>> >> >> >> > POL >> >>>> >> >> >> > POL >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > nstlist = 10 >> >>>> >> >> >> > ns_type = grid >> >>>> >> >> >> > pbc = xyz >> >>>> >> >> >> > rlist = 1.4 >> >>>> >> >> >> > >> >>>> >> >> >> > coulombtype = User >> >>>> >> >> >> > rcoulomb = 1.4 >> >>>> >> >> >> > >> >>>> >> >> >> > vdw_type = User >> >>>> >> >> >> > rvdw_switch = 1.0 >> >>>> >> >> >> > rvdw = 1.4 >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > tcoupl = V-rescale >> >>>> >> >> >> > tc_grps = Protein >> >>>> >> >> >> > tau_t = 0.1 >> >>>> >> >> >> > ref_t = 300 >> >>>> >> >> >> > pcoupl = no >> >>>> >> >> >> > >> >>>> >> >> >> > gen_vel = yes >> >>>> >> >> >> > gen_temp = 300 >> >>>> >> >> >> > gen_seed = -1 >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > constraints = none >> >>>> >> >> >> > constraint_algorithm = Lincs >> >>>> >> >> >> > unconstrained_start = no >> >>>> >> >> >> > lincs_iter = 1 >> >>>> >> >> >> > lincs_order = 4 >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > I am getting an error: get_simulation_setting: could not >> >>>> >> >> >> > fetch >> >>>> >> >> >> > table-extension from grompp.mdp and no default given, >> >>>> >> >> >> > please >> >>>> >> >> >> > add >> >>>> >> >> >> > it >> >>>> >> >> >> > in >> >>>> >> >> >> > there >> >>>> >> >> >> So you need to add the table-extension option to your mdp >> >>>> >> >> >> file. >> >>>> >> >> >> table-extension = 2.0 >> >>>> >> >> >> should work for you. >> >>>> >> >> > >> >>>> >> >> > >> >>>> >> >> > Can you please help with my mdp settings. I set: >> >>>> >> >> > >> >>>> >> >> > >> >>>> >> >> > energygrps = ACI BAS GLY NON POL >> >>>> >> >> > energygrp_table = ACI ACI ACI BAS ACI GLY ACI NON >> >>>> >> >> > ACI >> >>>> >> >> > POL >> >>>> >> >> > BAS >> >>>> >> >> > BAS >> >>>> >> >> > BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL >> >>>> >> >> > NON >> >>>> >> >> > POL >> >>>> >> >> > POL >> >>>> >> >> > table-extension = 2.4 ; its distance beyond the >> >>>> >> >> > largest >> >>>> >> >> > cuttoff >> >>>> >> >> > so should be 2.4 as 1.4 (cuttof) + 2.2 makes the table 3.8 >> >>>> >> >> > >> >>>> >> >> > >> >>>> >> >> > nstlist = 10 >> >>>> >> >> > ns_type = grid >> >>>> >> >> > pbc = xyz >> >>>> >> >> > rlist = 1.4 >> >>>> >> >> > rlistlong = 1.4 >> >>>> >> >> > >> >>>> >> >> > coulombtype = User >> >>>> >> >> > rcoulomb = 1.4 >> >>>> >> >> > >> >>>> >> >> > vdw_type = User >> >>>> >> >> > rvdw_switch = 1.0 >> >>>> >> >> > rvdw = 1.4 >> >>>> >> >> > >> >>>> >> >> > But then I get error that rvdw < the lenght of the table (3.8 >> >>>> >> >> > nm) >> >>>> >> >> > which >> >>>> >> >> > makes sense. If I then set up the rlistlong and rvdw to 3.8 >> >>>> >> >> > mdrun >> >>>> >> >> > gives >> >>>> >> >> > an >> >>>> >> >> > error: "Tables in file table_ACI_ACI.xvg not long enough for >> >>>> >> >> > cut-off: >> >>>> >> >> > should be at least 6.200000 nm" >> >>>> >> >> In the past people have ran simulations, where max (in >> >>>> >> >> settings.xml) >> >>>> >> >> and rvdw (in grompp.mdp) where not consistent. >> >>>> >> >> Same for table_end and (rvdw+table-extension). So we have added >> >>>> >> >> a >> >>>> >> >> minimum of consistency checks. >> >>>> >> >> Of course we cannot check all possible gromacs options and >> >>>> >> >> combinations. >> >>>> >> >> e.g. I don't even know if rvdw_switch works with tables at >> >>>> >> >> all. >> >>>> >> >> >> >>>> >> >> > >> >>>> >> >> > Would you please advise? Tutorials are supported by older >> >>>> >> >> > Gromacs >> >>>> >> >> > versions >> >>>> >> >> > as none of those settings are in the mdp file. >> >>>> >> >> All the tutorial should work with gromacs 4.6, I have tested >> >>>> >> >> some >> >>>> >> >> of >> >>>> >> >> them recently. >> >>>> >> >> >> >>>> >> >> But remember, whenever you don't put an option in the mdp file >> >>>> >> >> gromacs >> >>>> >> >> will use its internal defaults (see the gromacs manual) and the >> >>>> >> >> might >> >>>> >> >> lead to the error here. >> >>>> >> >> >> >>>> >> >> I would use: >> >>>> >> >> rvdw = 1.4 >> >>>> >> >> table-extension = 2 >> >>>> >> >> don't see >> >>>> >> >> rvdw_switch and rlistlong >> >>>> >> >> >> >>>> >> >> max = 1.4 >> >>>> >> >> table_end = 3.4 >> >>>> >> >> >> >>>> >> >> You could try to run the spce/ibi tutorial to see if something >> >>>> >> >> is >> >>>> >> >> wrong with your gromacs version. >> >>>> >> > >> >>>> >> > >> >>>> >> > Thank you. I am using 4.5.5. Looking at my distributions (RDF) >> >>>> >> > thy >> >>>> >> > go >> >>>> >> > to >> >>>> >> > zero just before 3 nm. Shall I set then: >> >>>> >> > >> >>>> >> > rvdw = 3.0 >> >>>> >> > table-extension = 4 ; >> >>>> >> > don't see >> >>>> >> > rvdw_switch and rlistlong >> >>>> >> > >> >>>> >> > max = 3 >> >>>> >> > table_end = 7 ; = 2*cutoff+1 >> >>>> >> > >> >>>> >> > >> >>>> >> > And my table will be from 0 to 7 then. Would that work? >> >>>> >> Looks good to me. >> >>>> > >> >>>> > >> >>>> > Getting an error in terms of the extrapolation: >> >>>> > >> >>>> > llegal division by zero at >> >>>> > /apps/votca/1.2.3/share/votca/scripts/inverse/table_extrapolate.pl >> >>>> > line 227. >> >>>> > >> >>>> > >> >>>> > ########################################################################################################################################################################################################################################## >> >>>> > # >> >>>> > # >> >>>> > # ERROR: >> >>>> > # >> >>>> > # do_external: subscript >> >>>> > /apps/votca/1.2.3/share/votca/scripts/inverse/table_extrapolate.pl >> >>>> > --function exponential --avgpoints 5 --region left >> >>>> > ACI-ACI.pot.smooth.13lKf >> >>>> > ACI-ACI.pot.extrapol2.tgLGm (from tags table extrapolate) failed # >> >>>> > # >> >>>> > # >> >>>> > >> >>>> > >> >>>> > ########################################################################################################################################################################################################################################## >> >>>> > >> >>>> > I tried making tables from csg_stat with maximum value if 3 and 7 >> >>>> > and >> >>>> > the >> >>>> > same appears. >> >>>> > >> >>>> > Any suggestions appreciated. >> >>>> Have a look at ACI-ACI.pot.smooth.13lKf to see if it looks ok. (Or >> >>>> post it on the list.) >> >>>> >> >>>> > llegal division by zero at >> >>>> > /apps/votca/1.2.3/share/votca/scripts/inverse/table_extrapolate.pl >> >>>> > line 227. >> >>>> line 227 contains: >> >>>> $grad_beg = ($val[$first + $avgpoints] - $val[$first])/($r[$first + >> >>>> $avgpoints] - $r[$first]); >> >>>> it can only be a division by zero error if $r[$first + $avgpoints] >> >>>> equals $r[$first], which would mean your table is screwed up. >> >>>> >> >>>> You might need to increase the min for the ACI-ACI as the >> >>>> extrapolation on the left fails. >> >>>> We have made VOTCA a bit smarter about that, but you will need to >> >>>> install the 1.3-dev version for that. >> >>>> >> >>>> > >> >>>> > Steven >> >>>> > >> >>>> > >> >>>> >> >> >>>> >> >> >>>> >> > >> >>>> >> > Steven >> >>>> >> >> >> >>>> >> >> >> >>>> >> >> >> >>>> >> >> > >> >>>> >> >> > >> >>>> >> >> > Steven >> >>>> >> >> > >> >>>> >> >> > >> >>>> >> >> >> >> >>>> >> >> >> >> >>>> >> >> >> > # >> >>>> >> >> >> > >> >>>> >> >> >> > I have table.xvg with "zeros" as well as all the files. >> >>>> >> >> >> > >> >>>> >> >> >> > Would you pelase advise? >> >>>> >> >> >> > >> >>>> >> >> >> > Steven >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > >> >>>> >> >> >> > -- >> >>>> >> >> >> > 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. >> >>>> >> >> > >> >>>> >> >> > >> >>>> >> >> >> >>>> >> >> >> >>>> >> >> >> >>>> >> >> -- >> >>>> >> >> 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. >> >>>> >> > >> >>>> >> > >> >>>> >> >> >>>> >> >> >>>> >> >> >>>> >> -- >> >>>> >> 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. >> >>>> > >> >>>> > >> >>>> >> >>>> >> >>>> >> >>>> -- >> >>>> 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. >> > >> > >> >> >> >> -- >> 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. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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