I have executed csg_stat on two trajectories (a) coarse-grained atomistic
trajectory and (b) trajectory after step_001 with the following commands:
(a) csg_stat --cg
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/pc_new_cg.xml
--options
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/settings_bon_nb.xml
--nt 8 --trj cg_traj.trr --top
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/step_001/topol.tpr
I obtain well behaved distribitions for each of the bonds.
(b) csg_stat --cg
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/pc_new_cg.xml
--options
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/settings_bon_nb.xml
--nt 8 --trj ../traj.xtc --top
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/step_001/topol.tpr
But for the step_001 trajectory, distributions for AB and DB are wiered. In
this trajectory the g_rdf and csg_boltzmann command works very fine.
I have no clue what wrong I am doing.
Because of the wiered behaviour of AB.bond.dist.new. I am getting following
error:
*****************************************************
working directory:
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/step_001'
Running critical command 'mktemp AB.bond.dist.tgt_extrapolated.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1
--region leftright AB.bond.dist.tgt_smooth.Ypjxs
AB.bond.dist.tgt_extrapolated.JWxob' (from tags table extrapolate) dir
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse
Running subscript 'dist_adjust.pl AB.bond.dist.tgt_extrapolated.JWxob
AB.bond.dist.tgt' (from tags dist adjust) dir
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse
Running subscript 'update_ibi_pot.pl AB.bond.dist.tgt AB.bond.dist.new
AB.bond.pot.cur AB.bond.dpot.pure_ibi' (from tags update ibi_pot) dir
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse
Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p'
Running subscript 'dpot_shift_bo.pl AB.bond.dpot.pure_ibi AB.bond.dpot.new'
(from tags dpot shift_bonded) dir
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse
No valid value found in AB.bond.dpot.pure_ibi at
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse/dpot_shift_bo.pl line
51.
Callstack:
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse/inverse.sh - linenumber
265
do_external - linenumber 171 in
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse/functions_common.sh
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse/update_ibi.sh -
linenumber 32
for_all - linenumber 17 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat
function do_external')
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse/update_ibi_single.sh -
linenumber 42
do_external - linenumber 22 (see 'csg_call
--cat function do_external')
die - linenumber 2 (see 'csg_call --cat
function die')
###########################################################################################################################################################################
#
#
#
ERROR:
#
# do_external: subscript
/opt/apps/votca/1.3-dev/share/votca/scripts/inverse/dpot_shift_bo.plAB.bond.dpot.pure_ibi
AB.bond.dpot.new (from tags dpot shift_bonded) failed
#
# For details see the logfile
/data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/inverse.log
#
#
#
###########################################################################################################################################################################
*****************************************************
Kindly suggest how to overcome this.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Aug 14, 2013 at 10:49 AM, Chandan Choudhury <[email protected]>wrote:
> Dear Christoph,
>
> Thanks for fixing the bug. I made the changes in the source code and
> re-installed votca (1.3-dev).
>
> The thing which has been troubling very much is the bonded distributions
> of AB and DB. The sequence of the polymer is A-B1-C1-D1-B2-C2-D2-B3-E. The
> other distributions (BC, CD and BE) shows the same behaviour as from the
> g_rdf (nrexcl=0) command. Infact, on using the csg_boltzmann on the
> trajectory of step_001, I obtain a well behaved distributions fo all the
> bond distributions. Infact plots are overlapping for BC, CD and BE (when
> compared with csg_stat).
> I donot understand why only these to bonds are behaving in a different
> way. I have attached the output of AB and DB bonds. AB contains -nan-.
>
> One way to get rid of it, I suppose would be to use csg_boltzmann tool.
> Can it be used for bonded part?
>
> Chandan
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Wed, Aug 14, 2013 at 3:34 AM, Christoph Junghans <[email protected]>wrote:
>
>> 2013/8/13 Christoph Junghans <[email protected]>:
>> > 2013/8/13 Chandan Choudhury <[email protected]>:
>> >>
>> >> 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.
>> > The bonded ibi feature in new in votca 1.3, it might not be very well
>> tested.
>> >
>> > I have the suspicion that the normalization for the bonded interaction
>> > might be inconsistent in csg_stat.
>> > Usually that has no effect on IBI as the only thing, which matters is
>> > the ratio, so it will works as long as the target distribution has the
>> > same normalization.
>> >
>> > I will have a look into it soon.
>> Actually, there was a bug! I fixed it:
>> <
>> https://code.google.com/p/votca/source/detail?r=ea8e40fb78693ba6fe2dd1d544aff6d6e111b845&repo=csg
>> >
>> and also updated the tutorials:
>> <
>> https://code.google.com/p/votca/source/detail?r=6e0f1991ad31eda3a86e660637f156a514f217a1&repo=csg-tutorials
>> >
>>
>> I didn't added the factor 1/r , 1/sin at this point, but for IBI that
>> didn't matter much as long as the target distribution is generated
>> with csg_stat, too.
>>
>> Christoph
>> >
>> > For all the other readers, bonded distribution in csg_boltzmann are
>> > correct and non-bonded distribution in csg_stat, too. The thing in
>> > question are bonded distribution from csg_stat!
>> >
>> >>
>> >> 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
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>> >> 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.
>> >>
>> >>
>> >
>> >
>> >
>> > --
>> > Christoph Junghans
>> > Web: http://www.compphys.de
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>> --
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>
>
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