Hey!
Can you please explain how exactly I can set and variate numerical
factor ai (0<ai<1) for U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)).
Because after 10 iteration instead of convergence I have a big
divergence. I've specified already simple pressure correction and it
works:
<cg>
...
<inverse>
<p_target>1</p_target>
<post_update>pressure</post_update>
<post_update_options>
<pressure>
<do>0 0 1</do>
<type>simple</type>
<simple>
<scale>0.0003</scale>
</simple>
</pressure>
</post_update_options>
Which update script I should use for this purpose and in which section
of settings.xml file I need to specify this option?
Thanks a lot in advance,
Sergio.
On Jul 10, 8:12 pm, "Victor Rühle" <[email protected]> wrote:
> Use the post update script scale and its corresponding option
>
> http://www.votca.org/Documentation/reference-cginteraction
> --
> Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.
>
> chemistry <[email protected]> schrieb:
>
> Hello! in U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)) where one can set numerical
> factor ai (0<ai<1). At the moment my calculation is diverges, so in general
> how one can reach better convergency? Kind regards, Sergio On Jul 7, 5:03 pm,
> Christoph Junghans <[email protected]> wrote: > 2011/7/7 chemistry
> <[email protected]>:> Is it possible do not use tables_*.xvg and instead
> of it set the > > parameters for bond, angle and dihedral to the topol.top
> with > > equilibrium bond length, angle and force constants. In this case
> ibi- > > procedure for my system works. > > Yes, if the potential can be
> reasonably approximated by a harmonic > form. Just compare the table to
> k/2*(r-r_0)^2 ! > > > And how one can choose the exact simulation time for
> one iteration for > > different systems? > > There is no rule. The iteration
> has to be long enough, so that the > distributions of the interactions, you
> want to iteratively refine, are > sampled reasonable. Too long iterations
> just waste your computer
> time > ;-) > I usually do 100 short iterations follow by 50 longer ones, but
> that > is my personal recipe. > > Cheers, > > Christoph > > > > > Thanks a
> lot in advance, > > Sergio > > > On Jul 5, 5:04 pm, Victor Ruehle
> <[email protected]> wrote: > >> Hey, > > >> 1) I recommend to use version 1.2.
> The functionality + arguments of > >> convert_potentials have slightly
> changed. > > >> 2) in the files you sent me, the bad sampled regions were not
> cut and > >> therefore the extrapolate failed (zoom in at table_a0.xvg where
> the > >> extrapolated region at the left starts). This will lead to a very >
> >> strong peak in the force and is probably what messes up your run. > >>
> Please make sure to really cut the very rough points at the left and > >>
> right of bonded potentials. This was done in the sed commands i send > >>
> you. Either adjust the number of points there or better skip this > >>
> command and do it manually. > > >> Victor > > >> 2011/7/5 chemistry
> <[email protected]>: > > >> > Hey,> > >> > the format of the table_*.xvg
> which was created after post-processing > >> > looks like this: > > >> >
> table_a1.xvg: > > >> > 0.0000000000e+00 8.6955642509e+07 0.0000000000e+00 >
> >> > 5.0000000000e-02 8.6862417509e+07 1.8640000000e+06 > >> >
> 1.0000000000e-01 8.6769242509e+07 1.8630000000e+06 > >> > 1.5000000000e-01
> 8.6676117509e+07 1.8620000000e+06 > >> > 2.0000000000e-01 8.6583042509e+07
> 1.8610000000e+06 > > >> > and yesterday I've created the same format of the
> table like in your > >> > case by myself. I used for this C-programing and
> described the > >> > potential with the help of harmonic potential. And now
> it works well. > > >> > new one table_a1.xvg: > > >> > 0.000000 1201.461834 0
> > >> > 0.050000 1200.343519 0 > >> > 0.100000 1199.225724 0 > >> > 0.150000
> 1198.108451 0 > >> > 0.200000 1196.991698 0 > > >> > In both cases the
> potentials look similar around the minimum. Is it > >> > possible that the
> GROMACS in someway cannot read correctly the > >> >
>
> table_*.xvg? > > >> > Kind regards, > >> > Sergio > > >> > On Jul 4, 7:50 pm,
> Victor Ruehle <[email protected]> wrote: > >> >> Hey, > > >> >> can you please
> attach your table_?.xvg > > >> >> Cheers, > >> >> Victor > > >> >> 2011/7/4
> chemistry <[email protected]>: > > >> >> > Hey, Victor! > > >> >> > With
> table_b1.xvg and table_a1.xvg from your tutorial simulation for > >> >> >
> propane works well. > >> >> > I'd tried to process the potentials for propane
> myself and after when > >> >> > I started the simulations I've got the same
> mistake like for my > >> >> > system: > > >> >> > "Fatal error: > >> >> > A
> tabulated bond interaction table number 1 is out of the table range: > >> >>
> > r 3.157974, between table indices 3157 and 3158, table length 501" > > >>
> >> > Seems that I have some problem with creating the tables_*.xvg > >> >> >
> Can you please check the way of post-processing of the potentials. > >> >> >
> At the beginning I had the same shape of the potential like in your > >> >> >
> case (I've got it with csg_boltzmann from all-atom MD simulation of > >> >> >
> propane at T=200 K): > > >> >> > bond: > > >> >> > sed -e '1,5d' -e 's/$/ i/'
> AB.pot | tac | sed -e '1,4d' | tac > AB.cut > >> >> > csg_call table smooth
> AB.cut AB.smooth > >> >> > csg_resample --in AB.smooth --out AB.refined
> --grid 0::0.001:0.5 > >> >> > csg_call table extrapolate --function quadratic
> AB.refined AB.pot.cur > >> >> > csg_call --options table.xml
> convert_potential xvg --type bonded > >> >> > AB.pot.cur table_b1.xvg > > >>
> >> > where table.xml: > > >> >> > <cg> > >> >> > <inverse> > >> >> >
> <gromacs> > >> >> > <pot_max>1e8</pot_max> > >> >> >
> <table_end>0.5</table_end> > >> >> > <table_bins>0.002</table_bins> > >>
> >> > </gromacs> > >> >> > </inverse> > >> >> > </cg> > > >> >> > angle:
> > > >> >> > sed -e 's/$/ i/' ABA_angle.pot | tac | sed -e '1,2d' | tac >
> ABA.cut > >> >> > awk '{print $1/3.141592654*180.0,$2,$3,$4}' ABA.cut >
> ABA.new.cut > >> >> > csg_call table
> smooth ABA.new.cut ABA.smooth > >> >> > csg_resample --in ABA.smooth --out
> ABA.refined --grid 0::0.05:180 > >> >> > csg_call table extrapolate
> --function quadratic ABA.refined > >> >> > ABA.pot.cur > >> >> > csg_call
> --options table.xml convert_potential xvg --type bonded > >> >> > ABA.pot.cur
> table_a1.xvg > > >> >> > where table.xml: > > >> >> > <cg> > >> >> >
> <inverse> > >> >> > <gromacs> > >> >> > <pot_max>1e8</pot_max> > >> >>
> > <table_end>180</table_end> > >> >> > <table_bins>0.05</table_bins>
> > >> >> > </gromacs> > >> >> > </inverse> > >> >> > </cg> > > >> >> > In
> both cases the potentials look similar around the minimum, but > >> >> >
> afterwords they are totally different. I wanted to get the same > >> >> >
> table_*.xvg like in your example. > > >> >> > Yours respectfully, > >> >> >
> Sergio > > >> >> > On Jul 1, 11:34 am, Victor Ruehle <[email protected]>
> wrote: > >> >> >> Be aware, if you have a bug in your coarse-grained
> topology, it might > >> >> >>
> immediately crash the simulations similar to the problem you > >> >> >>
> described. The csg_map will give a reasonable initial structure, this > >> >>
> >> should do well if your coarse-grained potentials are ok (eventually do >
> >> >> >> a steep before). The topology generation (csg_gmxtopol) just
> provides > >> >> >> a point to start from but will always require tuning by
> hand to put in > >> >> >> correct parameters. > > >> >> >> Also verify your
> mapping by loading atomistic + coarse-grained > >> >> >> structures in vmd. >
> > >> >> >> 2011/7/1 chemistry <[email protected]>: > > >> >> >> > Sorry,
> it was a problem with the internet and that's why I posted the > >> >> >> >
> same message twice. > > >> >> >> > I'm doing it in the same way how you
> wrote. So, I'll check all stuff > >> >> >> > again and thanks for fast
> answer. > > >> >> >> > Kind regards. > > >> >> >> > On Jul 1, 11:14 am,
> chemistry <[email protected]> wrote: > >> >> >> >> Hello! > > >> >> >> >>
> Seems that I have not a
> good initial CG-structure. I've got it with > >> >> >> >> the help of
> csg_map: > > >> >> >> >> $csg_map --top topol.tpr --trj traj.trr --cg
> mappin.xml --out cg.gro > > >> >> >> >> In my mappin.xml file every monomer
> of my system (P3HT) divided on the > >> >> >> >> three beads and each bead
> has a different name. > >> >> >> >> How exactly did you get initial
> CG-structure for propene in your > >> >> >> >> example? > > >> >> >> >>
> Thanks a lot in advance, > >> >> >> >> Sergio > > >> >> >> >> On Jun 30,
> 12:20 pm, Sebastian <[email protected]> wrote: > > >> >> >> >> > Hi
> 'chemistry', > > >> >> >> >> > it seems your bond is streching to far, this
> could be due to a too > >> >> >> >> > weak minimum in the bonded interaction
> or beacause your system > >> >> >> >> > explodes (too high energies) in some
> other part of the system. > >> >> >> >> > I would try: > >> >> >> >> > 1) run
> a steepest decent before the actual simulation > >> >> >> >> > 2) make the
> bonded table longer by filling up
> some zeroes. Then check > >> >> >> >> > if something else breaks (with a 'out
> of range') error.... > > >> >> >> >> > -Sebastian > > >> >> >> >> > On Jun
> 30, 10:34 am, chemistry <[email protected]> wrote: > > >> >> >> >> > >
> Hello! > > >> >> >> >> > > Thanks again for advices. It's helped me a lot. >
> >> >> >> >> > > I have already created all files what I need for CG
> calculation. But > >> >> >> >> > > now I have a problem with a tabulated bond
> interaction. I've checked > >> >> >> >> > > already this problem on the
> gromacs mailing-list. Unfortunately they > >> >> >> >> > > do not have any
> good advice there how to solve this problem. I would > >> >> >> >> > > be
> very grateful if you can give me some advice how to solve it. I > >> >> >> >>
> > > have next error message: > > >> >> >> >> > > "Fatal error: > >> >> >> >>
> > > A tabulated bond interaction table number 2 is out of the table range: >
> >> >> >> >> > > r 0.646802, between table indices 646 and 647, table length
> 501" > > >> >> >>
>
> >> > > Thanks a lot in advance, > >> >> >> >> > > Sergio. > > >> >> >> >> > >
> >> > > On Jun 27, 6:33 pm, Victor Ruehle <[email protected]> wrote: > > >> >>
> >> > > >> >> > > > Hey, > > >> >> >> >> > > > i also use csg_boltzmann, the
> >> > > tab command (dont forget tab set scale > >> >> >> >> > > > bond / tab
> >> > > set scale angle for bond/angles). some of my examples (the > >> >> >>
> >> > > >> > > > .pot files are the output of csg_boltzmann): > >> >> >> >> >
> >> > > > > bonds: > >> >> >> >> > > > cp ../../pot/AB_bond.pot . > >> >> >>
> >> > > >> > > > sed -e '1,5d' -e 's/$/ i/' AB_bond.pot | tac | sed -e '1,4d'
> >> > > | tac > > >> >> >> >> > > > AB.cut ; cut bad sampled regions at the
> >> > > boundaries > >> >> >> >> > > > csg_call table smooth AB.cut AB.smooth
> >> > > > >> >> >> >> > > > csg_resample --in AB.smooth --out AB.refined
> >> > > --grid 0::0.001:0.5 > >>
>
> ...
>
> read more »
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