Hi,
You have not explained your problem sufficiently. Your original issue
appears to be that you are getting less data out of your calculation
than you expect, but you give only vague descriptions of what you are
doing.
On Thu, Dec 31, 2020 at 5:46 AM MYRIAN TORRES RICO
<myriam.torres.iiq.csic.es> wrote:
>
> trajin /mnt/DISCO-EXTERNO/myriam/smp-199ptn4syn/smp-199ptn4rig_vcon3.mdcrd
How many frames does cpptraj suggest are in this trajectory (check the
output)? What is the trajectory format (ascii/netcdf)? If it is ascii,
are you sure you are using the correct topology file? How often did
you write the trajectory (i.e. what was ntwx) compared to your time
step (dt)? In general, the more details you provide, the more chance
someone has of helping you.
-Dan
>
> pucker p1 .2175 .2189 .2187 @2184 @2178 @2177 out pucker1.dat cremer
> amplitude theta range360
> pucker p2 .2200 .2216 .2212 .2210 .2203 @2202 out pucker2.dat cremer
> amplitude theta range360
> pucker p3 .2221 .2235 .2233 .2230 .2224 .2223 out pucker3.dat cremer
> amplitude theta range360
> pucker p4 .2246 @2262 @2258 @2256 @2249 @2248 out pucker4.dat cremer
> amplitude theta range360
> pucker p5 .2267 .2282 .2278 @2276 @2270 @2269 out pucker5.dat cremer
> amplitude theta range360
>
> Thanks in advance,
>
>
> Myriam
>
>
>
>
> David A Case <david.case.rutgers.edu> escribió:
>
> > On Wed, Dec 30, 2020, MYRIAN TORRES RICO wrote:
> >>
> >> I have a question about the data's treatment in pucker.in. I have
> >> obtained my file.crd of 80ns more less, but when I launch the
> >> puckering calculation and I represent the graphs in Origin, only 10ns
> >> appears...why? any idea?
> >
> > Does this happen only with pucker calculations? What happens if you use
> > the same trajin commands, but ask for something like distance? What
> > happens if you ask for fewer snapshots in the trajin commands? Don't be
> > afraid to experiment.
> >
> > Also, look at the file that cpptraj creates: does it have the expected
> > number of lines?
> >
> > Basically, there are many ways that one could get the behavior you
> > describe. (It could even that Origin doesn't understand the format.) If
> > you can't debug it yourself, you will need to post the exact commands you
> > gave to cpptraj.
> >
> > ...good luck....dac
> >
> > --
> >
> > ====================================================================
> > David A. Case | email:
> > Dept. of Chemistry & Chemical Biology | david.case.rutgers.edu
> > Rutgers University | skype: dacase
> > 174 Frelinghuysen Road, Rm. 208b | cell: +1-609-751-8668
> > Piscataway, NJ 08854 USA | web: casegroup.rutgers.edu
> > ====================================================================
> >
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>
>
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Received on Thu Dec 31 2020 - 06:30:02 PST
