Hello Christoph,
I have looked at the tutorial handouts and all the parts of the manual
and many forum discussions.
This is what I am understanding so far (step 1 and 2 are complete):
1. To map from the atomistic to coarse-grained:
csg_map --top topol.tpr --trj confout.gro --cg propane.xml --out
conf_cg.gro
2. To make the coarse grained topology file:
csg_gmxtopol --top topol.tpr --cg propane.xml --out out.top
3. To calculate distributions:
csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --nt 3 --
options fmatch.xml
Output files: CH2-CH3.dist.new, CH2-CH3.dist.new ,CH2-
CH3.dist.new, bond.dist.new, angle.dist.new
Some of these files will be renamed in the IBI CG run to:
CH2-CH3.dist.tgt, CH2-CH3.dist.tgt, CH2-CH3.dist.tgt
What use are these files then?: bond.dist.new, angle.dist.new
4. To calculate the potentials (I do not want to do it manually):
csg_boltzmann --top topol.tpr --trj traj.trr --cg propane.xml
Output files: angle.dist.ib, angle.pot.ib, bond.dist.ib,
bond.pot.ib
(a) manually delete poorly sampled parts of: "bond.pot.ib" to
"bond.pot.ib_new"
and "angle.pot.ib" to "angle.pot.ib_new"
(b) Execute the following commands to convert to the formatting of
Gromacs:
csg_call --options bond.xml --ia-type bonded
convert_potential gromacs bond.pot.ib_new table_b1.xvg
csg_call --options angle.xml --ia-type bonded
convert_potential gromacs bond.pot.ib_new table_a1.xvg
The shape of these 2 graphs are similar to what you have in
the tutorial but the numbers are different??
5. Coarse-grained run:
(a) Copy table.xvg from an example
(b) Copy table_b1.xvg and table_a1.xvg from step 4 as well as the
CG coordinates and topology files
(c) Execute the following command which will run the CG simulation
and produce new files and tables:
(e.g. table_CH2-CH3.xvg, table_CH2-CH3.xvg, table_CH2-CH3.xvg
as specified in the settings file)
csg_inverse --options settings.xml
Parts of step 3 - 5 are not correct in my understanding for sure
otherwise everything will be fine and this is what we would discuss.
Perhaps others on the forum can clarify where I am missing the linking
in the above 5 steps.
Thanks again for your time and help.
Tinashe
On Jan 21, 10:44 pm, Christoph Junghans <[email protected]> wrote:
> Am 20. Januar 2012 09:41 schrieb Tinashe <[email protected]>:> Before I
> do what you have suggested, I do not know yet 100% how to get
> > both bonded and non-bonded potentials in VOTCA "correctly".
>
> > 1. For instance, how do you obtain the table.pot file?
> > This file is needed to start the following sequence of commands:
>
> I guess, you are speaking about those non-bonded interaction which are
> not iterated, usually named table.xvg and table_X_Y.xvg in the
> maindir.
>
> table.xvg is Gromacs standard interaction table for all non-bonded
> interaction, which are not covered by the pairs listed in
> energygrp_table of your mdp file.
> In all examples of csg-tutorial this file has no meaning as all
> interaction are covered by energygrp_table, so you can fill it with
> zeros. However gromacs still needs it. (see Gromacs Manual for
> details)
>
> table_X_Y.xvg, where X and Y are groups from energygrps of your mdp file,
> can come for a former ibi simulation or somewhere else. These are only
> needed if you do a iteration of only some of the non-bonded
> interactions, no csg tutorial does that.
>
>
>
> > csg_sample --in table.pot --out table_resample.pot --grid min:step:max
> > csg_call table extrapolate table_resample.pot table_extrapolate.pot
> > csg_call --options table.xml convert_potential gromacs
> > table_extrapolate.pot table.xvg
>
> > 2. Similarly, how do I obtain the table.pot for both the bonded and
> > angle potentials
> > which I will resample, extrapolate and later convert to table_b1.xvg
> > and table_a1.xvg?
>
> These are bonded interactions. See chapter 5 of the manual on how to
> calculate them. Basically you do simple Boltzmann inversion using
> csg_boltzmann or a simple script.
>
>
>
> > Is the way of obtaining the target non-bonded potentials for the IBI
> > method through force matching (csg_fmatch)
> > or are the potentials only supposed to be derived using csg_stat and/
> > or csg_boltzmann?
>
> IBI aims to reproduce distributions (structure based coarse-graining), while
> force matching aims to reproduce force.
>
> csg_stat only calculates bonded and non-bonded distributions.
> csg_boltzmann calculates bonded distribution and other analysis
> including Boltzmann inversion.
>
> Christoph
>
>
>
>
>
>
>
> > Perhaps a step-by-step explanation will help me to reproduce your
> > hexane tutorial and serve to help the other new VOTCA users as well.
>
> > Thanks a lot.
>
> > Tinashe
>
> > On Jan 18, 9:36 pm, Christoph Junghans <[email protected]> wrote:
> >> Hi Tinashe,
>
> >> welcome!
>
> >> Am 18. Januar 2012 07:18 schrieb Tinashe <[email protected]>:> - the
> >> min/max/step values for force matching i get from the
> >> > distribution functions, that it samples a valid interval, and the
> >> > number of bins is not too high, otherwise might become slow
> >> > - the table_a1*.xvg are usually generated using csg_boltzmann, there
> >> > is a section in the manual. You can convert the votca potential files
> >> > to gromacs using csg_call. I have to lookup the correct command, but
> >> > christoph might answer on googlrgroups.
>
> >> See section 4.2 of the manual:
> >> <https://votca.googlecode.com/files/votca-csg-manual-1.2.2.pdf>
>
> >> But basically once you have the potential in Votca format, it boils
> >> down to the following:
> >> -create a simple settings xml file (table.xml):
> >> <cg>
> >> <inverse>
> >> <gromacs>
> >> <pot_max>1e8</pot_max>
> >> <table_end>8.0</table_end>
> >> <table_bins>0.002</table_bins>
> >> </gromacs>
> >> </inverse>
> >> </cg>
> >> and run
> >> $csg_call --ia-type TYPE --options table.xml convert_potential gromacs \
> >> table_extrapolate.pot table.xvg
> >> where type can be non-bonded, bonded, angle, dihedral.
>
> >> Note, that in the current development version we renamed "bonded" to
> >> "bond"!
>
> >> Cheers,
>
> >> Christoph
>
> >> > - renaming te distribution function and use it as target is the proper
> >> > way to do
> >> > - you can make a few optimizations in the grompp, e.g. if you don't
> >> > have charge in the cg model, use cut-off as estatic method. this will
> >> > disable the fft from pme.
>
> >> > Best,
> >> > Victor
>
> >> >> Dear Victor,
>
> >> >> Firstly, thanks a lot, your suggestions were on the mark.
>
> >> >> At first, I ran the following command:
> >> >> csg_stat --top topol.tpr --trj traj.trr --cg hexane.xml --nt 3 --options
> >> >> fmatch.xml
> >> >> and then renamed the files from *.dist.new to *.dist.tgt to use together
> >> >> with the settings file. Is this the correct way to things?
>
> >> >> How are the following files meant to be created: table.xvg table_a1.xvg
> >> >> table_b1.xvg
> >> >> Where does one get the numbers in the settings.xml and fmatch.xml? I
> >> >> have
> >> >> simply used numbers from VOTCA tutorials?
> >> >> It appears that I can still use the same grommp file as the one I used
> >> >> for
> >> >> atomistic simulations, is this so?
>
> >> >> Kind regards,
> >> >> Tinashe
>
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> >> --
> >> Christoph Junghans
> >> Web:http://www.compphys.de-Hide quoted text -
>
> >> - Show quoted text -
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> Christoph Junghans
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>
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