Hi Sikandar
Attached are inverse.log file and settings.xml files.
Thank you
Marc
On Tue, May 6, 2014 at 9:02 PM, Sikandar Mashayak <[email protected]>wrote:
> Hi Marc
>
> Can you please send inverse.log file? It will have more details about the
> failure.
>
> Thanks
> Sikandar
>
>
> On Tue, May 6, 2014 at 5:40 PM, Marc Segovia <[email protected]>wrote:
>
>> Hi Sikandar
>>
>> You are right the rdf are converged in spce/water.
>>
>> Now I move to other model, I fit settings.xml script, include as guess a
>> initial value from ibi previous, but an old problem appears.
>>
>> "table_average.sh: averaging with awk failed"
>>
>> I saw in mailing list, this is an issue related with a mismatch in
>> param.cur, same happens in my case, steep-001 runs well, but in 002
>> colapse, both files mismatch, different number of parameters.
>>
>> My develpement version is 1.88, from 19.10.2013, maybe this wasn't solved
>> yet , so I need to update my dev version ?
>>
>>
>> Thanking in advance by your help
>>
>> Best Regards
>> Marc
>>
>>
>> On Sat, May 3, 2014 at 1:29 PM, Sikandar Mashayak
>> <[email protected]>wrote:
>>
>>> Hi Marc
>>>
>>> Did you check the CG-CG RDF at 300the step? How do they compare with the
>>> reference RDF?
>>>
>>> In my experience, I found that, in the case of bulk water, with the
>>> current RE minimization method in VOTCA,
>>> the CG potentials more or less converge to the values which reproduce
>>> target RDF in less than 200 iterations.
>>> However, due to statistical nature of short CG-MD simulations at every
>>> update step, the values of CG potentials
>>> fluctuate around the converged values. These fluctuations may or may not
>>> satisfy the convergence check criteria, i.e., they may be smaller or larger
>>> than the specified tolerance, and it depends on various setting parameters
>>> such as length of CG-MD simulations, relaxation parameters, and number of
>>> knot values.
>>>
>>> Therefore, it is always good to check the CG particle RDFs periodically
>>> to judge whether the RE minimization is
>>> converged or not. I guess, in VOTCA, there is a way to use CG particle
>>> RDFs as a measure to decide convergence. I will check how to do that and
>>> get back to you.
>>>
>>> We are also working on implementing alternative approach for RE
>>> minimization, which is a deterministic approach. It is based on reweighting
>>> strategy. You can read more about it in the article
>>>
>>> Chaimovich, Aviel, and M. Scott Shell. “Coarse-Graining Errors and
>>> Numerical Optimization Using a Relative Entropy Framework.” *The
>>> Journal of Chemical Physics* 134, no. 9 (March 3, 2011): 094112.
>>> doi:10.1063/1.3557038
>>>
>>> I hope it helps. Let us know if you have any further questions or
>>> suggestions.
>>>
>>> Thanks,
>>> Sikandar
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Fri, May 2, 2014 at 4:31 PM, Marc Segovia <[email protected]>wrote:
>>>
>>>> Hi
>>>>
>>>> Last days I run relative entropy tutorial, using votca 1.3, in spce
>>>> water model
>>>> After several days in my PC, finally the cg don't converge.
>>>>
>>>> step 300 done, needed 1083 secs
>>>> Doing convergence check: default
>>>> Iterations are not converged, going on
>>>>
>>>> My question is , this happens because a convergence of 0.001 is to
>>>> small, or because numerical errors in my software or because the number of
>>>> configuration to average is too low , 50 ? or something else.
>>>>
>>>> Thanking in advance by your help
>>>>
>>>> Best Regards
>>>>
>>>> Marc
>>>>
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>>>
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>>
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<!-- options to perform relative entropy iterations -->
<cg>
<!-- non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>A-A</name>
<!-- specify type of CG pair -->
<type1>A</type1>
<type2>A</type2>
<!-- min, max and step size distance for pot (max=cutoff) -->
<min>0.0</min>
<max>0.9</max>
<step>0.002</step>
<re>
<!-- function form for the potential (lj126 or ljg or cbspl)-->
<function>cbspl</function>
<cbspl>
<!-- no. of knots for cbspl function -->
<nknots>48</nknots>
<core>extrapolate</core>
</cbspl>
<!-- distance range for the potential -->
<min>0.22</min>
<max>0.9</max>
</re>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>A-A.dist.tgt</target>
<gromacs>
<!-- name of the table for gromacs run -->
<table>table_A_A.xvg</table>
</gromacs>
<!-- do convergence -->
<post_add>acc_convergence average</post_add>
<post_add_options>
<!-- convergence check options -->
<convergence>
<!-- for RE we check change in potentials/parameters (new-cur) -->
<what>pot</what>
<weight>1.0</weight>
<base>cur</base>
<norm>2</norm>
</convergence>
<average>
<what>param pot</what>
</average>
</post_add_options>
</inverse>
</non-bonded>
<inverse>
<!-- System T = 300*0.00831451 kBT units -->
<kBT>2.4942</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>0</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>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg index.ndx</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<!-- ibi: inverse biltzmann imc: inverse monte carlo re: relative entropy-->
<method>re</method>
<!-- relative entropy specific options -->
<re>
<!-- relaxation parameter in Newton-Raphson update -->
<relax>0.7</relax>
</re>
<!-- convergence check options -->
<convergence_check>
<type>default</type>
<limit>0.0001</limit>
</convergence_check>
<average>
<steps>50</steps>
</average>
<!-- directory for user scripts -->
<scriptdir></scriptdir>
</inverse>
</cg>
<!-- options to perform relative entropy iterations -->
<cg>
<!-- non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>A-A</name>
<!-- specify type of CG pair -->
<type1>A</type1>
<type2>A</type2>
<!-- min, max and step size distance for pot (max=cutoff) -->
<min>0.0</min>
<max>0.9</max>
<step>0.002</step>
<re>
<!-- function form for the potential (lj126 or ljg or cbspl)-->
<function>cbspl</function>
<cbspl>
<!-- no. of knots for cbspl function -->
<nknots>48</nknots>
<core>extrapolate</core>
</cbspl>
<!-- distance range for the potential -->
<min>0.30</min>
<max>0.9</max>
</re>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>A-A.dist.tgt</target>
<gromacs>
<!-- name of the table for gromacs run -->
<table>table_A_A.xvg</table>
</gromacs>
<!-- do convergence -->
<post_add>acc_convergence average</post_add>
<post_add_options>
<!-- convergence check options -->
<convergence>
<!-- for RE we check change in potentials/parameters (new-cur) -->
<what>pot</what>
<weight>1.0</weight>
<base>cur</base>
<norm>2</norm>
</convergence>
<average>
<what>param pot</what>
</average>
</post_add_options>
</inverse>
</non-bonded>
<inverse>
<!-- System T = 300*0.00831451 kBT units -->
<kBT>2.4942</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>0</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>2.0</table_end>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg index.ndx</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<!-- ibi: inverse biltzmann imc: inverse monte carlo re: relative entropy-->
<method>re</method>
<!-- relative entropy specific options -->
<re>
<!-- relaxation parameter in Newton-Raphson update -->
<relax>0.7</relax>
</re>
<!-- convergence check options -->
<convergence_check>
<type>default</type>
<limit>0.0001</limit>
</convergence_check>
<average>
<steps>50</steps>
</average>
<!-- directory for user scripts -->
<scriptdir></scriptdir>
</inverse>
</cg>
