2013/7/9 <[email protected]>: > 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 I just took this rdf and ran "csg_call prepare_single ibi" manually and it works. Using this rdf in spce/ibi together with max=2.0 (from your setting file) also works!
> > > > 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.
