Hi Daniel,
My problem is, the frames that I expect are 40000 (nstlim/ntwr), and
when I calculate pucker, distances...with cpptraj, it only takes 11783
frames (one of the examples), but in others simulations don't happen
this, and I don't know why...(I hope it is understood).
Thanks in advance,
Myriam
Daniel Roe <daniel.r.roe.gmail.com> escribió:
> 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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Received on Thu Dec 31 2020 - 07:00:02 PST
