Hi Daniel,
I have probed this calculation for distances, and other files.crd and
ever It takes 15% of all frames approximately...and also I probed
other program different to origin, and the result is the same...Any
suggest? Is there another method to calculate puckering? This is my
script:
trajin /mnt/DISCO-EXTERNO/myriam/smp-199ptn4syn/smp-199ptn4rig_vcon3.mdcrd
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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Received on Thu Dec 31 2020 - 03:00:02 PST
