Dear users, I am using votca version 1.3-dev for cg simulation. At step_001, after the simulation by gromacs, csg_stat runs and it computes the distributions (reads the setting.xml and mapping_cg.xml).
My system and 5 different beads with 5 bond and 5 angles. While surprisingly, csg_stat produces incorrect distributions for the AB.bond and DB.bond (xvg attached). As a cross check, I executed the same csg_stat command on the cg trajectory, which was generated from atomistic simulations (with same setting amd mapping files). The command executes and the plots are reasonable. So, the mapping and setting files are correct. Also, I have used the g_rdf (with exclusion 0), to compute the bond distributions. The distributions for BC, CD and BE matches while for AB and DB bonds, it didnot match. I cannot undestand where I am mistaken. Kindly suggest me. N.B: I have also attached the settings and mapping files. -- Chandan kumar Choudhury NCL, Pune INDIA -- 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.
AB.bond.dist.new
Description: Binary data
DB.bond.dist.new
Description: Binary data
<cg>
<bonded>
<!-- name of the interaction -->
<name>AB.bond</name>
<min>0.42</min>
<max>0.52</max>
<step>0.005</step>
<inverse>
<!-- target distribution -->
<target>AB.bond.dist.tgt</target>
<gromacs>
<table>table_b0.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<name>BC.bond</name>
<min>0.32</min>
<max>0.40</max>
<step>0.005</step>
<inverse>
<!-- target distribution -->
<target>BC.bond.dist.tgt</target>
<gromacs>
<table>table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<name>CD.bond</name>
<min>0.34</min>
<max>0.45</max>
<step>0.005</step>
<inverse>
<!-- target distribution -->
<target>CD.bond.dist.tgt</target>
<gromacs>
<table>table_b2.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<name>DB.bond</name>
<min>0.40</min>
<max>0.52</max>
<step>0.005</step>
<inverse>
<!-- target distribution -->
<target>DB.bond.dist.tgt</target>
<gromacs>
<table>table_b3.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- name of the interaction -->
<name>BE.bond</name>
<min>0.32</min>
<max>0.40</max>
<step>0.005</step>
<inverse>
<!-- target distribution -->
<target>BE.bond.dist.tgt</target>
<gromacs>
<table>table_b4.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- name of the interaction -->
<name>ABC.angle</name>
<min>1.1</min>
<max>3.1</max>
<step>0.05</step>
<inverse>
<!-- target distribution -->
<target>ABC.angle.dist.tgt</target>
<gromacs>
<table>table_a0.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- name of the interaction -->
<name>BCD.angle</name>
<min>2.0</min>
<max>3.1</max>
<step>0.05</step>
<inverse>
<!-- target distribution -->
<target>BCD.angle.dist.tgt</target>
<gromacs>
<table>table_a1.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- name of the interaction -->
<name>CDB.angle</name>
<min>1.7</min>
<max>3.1</max>
<step>0.05</step>
<inverse>
<!-- target distribution -->
<target>CDB.angle.dist.tgt</target>
<gromacs>
<table>table_a2.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- name of the interaction -->
<name>DBC.angle</name>
<min>1.1</min>
<max>3.1</max>
<step>0.05</step>
<inverse>
<!-- target distribution -->
<target>DBC.angle.dist.tgt</target>
<gromacs>
<table>table_a3.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<!-- name of the interaction -->
<name>DBE.angle</name>
<min>1.1</min>
<max>3.1</max>
<step>0.05</step>
<inverse>
<!-- target distribution -->
<target>DBE.angle.dist.tgt</target>
<gromacs>
<table>table_a4.xvg</table>
</gromacs>
</inverse>
</bonded>
<non-bonded>
<!-- name of the interaction -->
<name>A-A</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>A</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>A-A.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_A.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>A-B</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>B</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>A-B.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 1 0</do_potential>
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_B.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>A-C</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>C</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>A-C.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_C.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>A-D</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>D</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>A-D.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_D.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>A-E</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>E</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>A-E.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 1 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_E.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>B-B</name>
<!-- types involved in this interaction -->
<type1>B</type1>
<type2>B</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>B-B.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_B_B.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>B-C</name>
<!-- types involved in this interaction -->
<type1>B</type1>
<type2>C</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>B-C.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_B_C.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>B-D</name>
<!-- types involved in this interaction -->
<type1>B</type1>
<type2>D</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>B-D.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 1 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_B_D.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>B-E</name>
<!-- types involved in this interaction -->
<type1>B</type1>
<type2>E</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>B-E.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 1</do_potential>
<!-- additional post processing of U after dU added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_B_E.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>C-C</name>
<!-- types involved in this interaction -->
<type1>C</type1>
<type2>C</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>C-C.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_C_C.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>C-D</name>
<!-- types involved in this interaction -->
<type1>C</type1>
<type2>D</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>C-D.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 1 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_C_D.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>C-E</name>
<!-- types involved in this interaction -->
<type1>C</type1>
<type2>E</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>C-E.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_C_E.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>D-D</name>
<!-- types involved in this interaction -->
<type1>D</type1>
<type2>D</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>D-D.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_D_D.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>D-E</name>
<!-- types involved in this interaction -->
<type1>D</type1>
<type2>E</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>D-E.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 1 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_D_E.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>E-E</name>
<!-- types involved in this interaction -->
<type1>E</type1>
<type2>E</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.00</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>E-E.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_add_options>convergence</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_E_E.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- 480*0.00831451 gromacs units -->
<kBT>3.99096</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>10</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.002</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>1000000</pot_max>
<!-- extend the tables to this value -->
<table_end>2.5</table_end>
<grompp>
<bin>grompp_463</bin>
</grompp>
<mdrun>
<command>mdrun_463 </command>
<checkpoint>state.cpt</checkpoint>
</mdrun>
</gromacs>
<map>pc_new_cg.xml</map>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg index.ndx</filelist>
<!-- do so many iterations -->
<iterations_max>50</iterations_max>
<convergence_check>
<type>default</type>
<limit>0.001</limit>
</convergence_check>
<!-- ibm: inverse biltzmann imc: inverse monte carlo -->
<method>ibi</method>
<!-- write log to this file -->
<log_file>inverse.log</log_file>
<!-- write restart step to this file -->
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
<cg_molecule>
<name>POLCAR</name>
<ident>polycarbonate</ident>
<topology>
<cg_beads>
<cg_bead>
<name>A</name>
<type>A</type>
<mapping>UNITY</mapping>
<beads> 1:RES:A </beads>
</cg_bead>
<cg_bead>
<name>B1</name>
<type>B</type>
<mapping>UNITY</mapping>
<beads> 1:RES:B1 </beads>
</cg_bead>
<cg_bead>
<name>C1</name>
<type>C</type>
<mapping>UNITY</mapping>
<beads> 1:RES:C1 </beads>
</cg_bead>
<cg_bead>
<name>D1</name>
<type>D</type>
<mapping>UNITY</mapping>
<beads> 1:RES:D1 </beads>
</cg_bead>
<cg_bead>
<name>B2</name>
<type>B</type>
<mapping>UNITY</mapping>
<beads> 1:RES:B2 </beads>
</cg_bead>
<cg_bead>
<name>C2</name>
<type>C</type>
<mapping>UNITY</mapping>
<beads> 1:RES:C2 </beads>
</cg_bead>
<cg_bead>
<name>D2</name>
<type>D</type>
<mapping>UNITY</mapping>
<beads> 1:RES:D2 </beads>
</cg_bead>
<cg_bead>
<name>B3</name>
<type>B</type>
<mapping>UNITY</mapping>
<beads> 1:RES:B3 </beads>
</cg_bead>
<cg_bead>
<name>E</name>
<type>E</type>
<mapping>UNITY</mapping>
<beads> 1:RES:E </beads>
</cg_bead>
</cg_beads>
<cg_bonded>
<bond>
<name>AB.bond</name>
<beads>
A B1
</beads>
</bond>
<bond>
<name>BC.bond</name>
<beads>
B1 C1
B2 C2
</beads>
</bond>
<bond>
<name>CD.bond</name>
<beads>
C1 D1
C2 D2
</beads>
</bond>
<bond>
<name>DB.bond</name>
<beads>
D1 B2
D2 B3
</beads>
</bond>
<bond>
<name>BE.bond</name>
<beads>
B3 E
</beads>
</bond>
<angle>
<name>ABC.angle</name>
<beads>
A B1 C1
</beads>
</angle>
<angle>
<name>BCD.angle</name>
<beads>
B1 C1 D1
B2 C2 D2
</beads>
</angle>
<angle>
<name>CDB.angle</name>
<beads>
C1 D1 B2
C2 D2 B3
</beads>
</angle>
<angle>
<name>DBC.angle</name>
<beads>
D1 B2 C2
</beads>
</angle>
<angle>
<name>DBE.angle</name>
<beads>
D2 B3 E
</beads>
</angle>
</cg_bonded>
</topology>
<maps>
<map>
<name>UNITY</name>
<weights> 1</weights>
</map>
</maps>
</cg_molecule>
