Re: [votca] Debugging IBI simulation with nonbonded and bonded interaction in coarse-grained solvent

[Christoph Junghans]

On Sat, Aug 21, 2021 at 10:13 PM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> Hello,
>
> I am running a coarse-grained simulation of a 3-bead molecule (2 bonds+1 angle) in a coarse-grained, single-bead, solvent (water) bath. I have successfully run the gromacs all-atom trajectories, and I am using votca to run the IBI simulation.
>
> From the all atom simulation, I obtained the solvent-solvent rdf, the 2 bond distributions, and the single angle distributions using csg_stat and csg_boltzmann.
>
> Then, I am running:
> csg_inverse --options settings.xml
>
> where settings.xml is:
> <cg>
> <non-bonded>
> <name>TW-TW</name>
> <!-- types of molecules involved in this interaction -->
> <type1>TW</type1>
> <type2>TW</type2>
> <!-- dimensions + grid spacing of tables for calculations -->
> <min>0</min>
> <max>1.4</max>
> <step>0.01</step>
> <inverse>
> <!-- target distribution (rdf) -->
> <target>TW-TW.dist.tgt</target>
> <!-- update cycles -->
> <do_potential>1</do_potential>
> <!-- additional post processing of dU before added to potential -->
> <post_update>scale smooth</post_update>
> <post_update_options>
> <scale>1</scale> <!-- scale the potentials before updating it -->
> <smooth>
> <iterations>2</iterations>
> </smooth>
> </post_update_options>
> <post_add></post_add>
> <gromacs>
> <table>table_TW_TW.xvg</table>
> </gromacs>
> </inverse>
> </non-bonded>
>
> <bonded>
> <name>BO1</name>
> <min>0.217</min>
> <max>0.253</max>
> <step>0.001</step>
> <inverse>
> <target>BO1.dist.tgt</target>
> <gromacs>
> <table>table_BO1.xvg</table>
> </gromacs>
> </inverse>
> </bonded>
> <bonded>
> <name>BO2</name>
> <min>0.227</min>
> <max>0.288</max>
> <step>0.001</step>
> <inverse>
> <target>BO2.dist.tgt</target>
> <gromacs>
> <table>table_BO2.xvg</table>
> </gromacs>
> </inverse>
> </bonded>
> <bonded>
> <name>ANG1</name>
> <min>1.877</min>
> <max>2.998</max>
> <step>0.001</step>
> <inverse>
> <target>ANG1.dist.tgt</target>
> <gromacs>
> <table>table_ANG1.xvg</table>
> </gromacs>
> </inverse>
> </bonded>
>
> <!-- general options for inverse script -->
> <inverse>
> <kBT>2.7437884</kBT>
> <program>gromacs</program>
> <map>1nipam.xml</map>
> <map>water.xml</map>
> <gromacs>
> <equi_time>20</equi_time>
> <table_bins>0.001</table_bins>
> <pot_max>1000000</pot_max>
> <table_end>2.5</table_end>
> <mdrun>
> <opts>-nt 8</opts>
> </mdrun>
> </gromacs>
> <filelist>grompp.mdp topol.top table.xvg index.ndx table_a1.xvg table_b1.xvg</filelist>
> <!-- do so many iterations -->
> <iterations_max>5</iterations_max>
> <convergence_check>
> <type>default</type>
> <limit>0.001</limit>
> </convergence_check>
> <method>ibi</method>
> <log_file>inverse.log</log_file>
> <restart_file>restart_points.log</restart_file>
> </inverse>
> </cg>
> I am getting the following error:
>
> # critical: 'csg_stat --nt 28 --options settings.xml --top topol.tpr --trj traj.xtc --begin 20 --first-frame 0 --cg "1nipam.xml;water.xml";' failed #
>
> After I go in step_001 and try the above command, I get:
>
> I get a wall of text saying:
>
> WARNING: unknown molecule "WT" with id XXXX in topology
>
> molecule will not be mapped to CG representation
>
> Check weather a mapping file for all molecule exists, was specified in --cg separated by ; and the ident tag in xml-file matches the molecule name.
>
> Topology does not have beads of type "TW"
> This was specified in type1 of interaction "TW-TW"
>
> I don't understand where this message is coming from. I have a 1nipam.xml file which has the information about the CG of my monomer molecule, and water.xml file which has the information about the CG scheme of my water molecule.
>
>
> I would appreciate any advice you have for me.
I would look at the mapping file agian, it seems after the 1:1 mapping
there is a "WT" in the topology (see the unknown molecule warning
above) , but in your settings.xml you are referring to TW, so my guess
you either want to change the water to "TW" in water.xml or "WT" in
the settings.xml.

Top debug this you can run:
csg_dump --top topol.tpr --cg "1nipam.xml;water.xml"
and check what votca reads.

Christoph
>
>
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--
Christoph Junghans
Web: http://www.compphys.de

[Satyen Dhamankar]

Hi Christoph, thank you, I figured it out. 

It required edits in the grompp energygrps in the gromacs.mdp.