OK I understand.
Thanks for the explanation !
Best wishes,
Marek
Dne Wed, 15 Aug 2012 22:29:34 +0200 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> Hi,
>
> I've got it figured out - the problem here resulted specifically from
> the fact that the first restart file you read in has no velocity
> information, while the rest of the restart files did. This is a
> problem that could only happen when reading a series of restarts with
> the first restart not having velocity info and any following restarts
> having velocity.
>
> Internally what happened is that since the first restart had no
> velocity, cpptraj didnt allocate space for velocities. This meant
> there was no space allocated for velocity info for subsequent
> restarts, since the parm never changed (which would normally trigger a
> reallocation of the frame). This in turn meant that after the first
> restart was read (correctly), subsequent restarts were read as if they
> had no velocities, i.e. the first line of velocity was being read as
> box coords, which in turn led to the nasty behavior you saw.
>
> Since ptraj doesn't try to read velocities it did not have this issue.
>
> I am working on a bugfix now. Thanks again for the report.
>
> -Dan
>
> On Wed, Aug 15, 2012 at 1:55 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>> Hi,
>>
>> Actually the problem isn't with cpptraj imaging; there is something
>> odd going on when cpptraj reads the restart file
>> P-G3-PROTONATED15proc.inpcrd first (if it is read in any other spot
>> things appear fine). For some reason when that is read first the box
>> coordinates of subsequent reads are corrupted somehow, which leads to
>> centering/imaging problems etc. I'll keep digging and let you know
>> what I find. Thanks for the test case.
>>
>> -Dan
>>
>> On Wed, Aug 15, 2012 at 12:21 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>>> OK,
>>>
>>> as I said the problem is in cpptraj IMAGE routine, the radgyr/drms
>>> "failure" is just
>>> the consequence ...
>>>
>>> Best wishes,
>>>
>>> Marek
>>>
>>>
>>>
>>>
>>> Dne Wed, 15 Aug 2012 19:49:18 +0200 Daniel Roe <daniel.r.roe.gmail.com>
>>> napsal/-a:
>>>
>>>> Hi,
>>>>
>>>> On Wed, Aug 15, 2012 at 4:11 AM, Marek Maly <marek.maly.ujep.cz>
>>>> wrote:
>>>>> Yes I know the difference but with DRMSD I had problem in case of
>>>>> PTRAJ
>>>>>
>>>>> ---------------------------------------------------------------------
>>>>> PTRAJ: drmsd :CEN,REC,REP,REE,ENP,EN0 first out DEN_RST.RMSD.RMSD
>>>>>
>>>>> WARNING in dispatchToken: Token string "drmsd" not found in tokenlist
>>>>
>>>> Oh, I didn't understand you initially, sorry. The issue here is that
>>>> drmsd is in cpptraj only.
>>>>
>>>> I have received the test case (thanks!); I'll check it out and get
>>>> back to you shortly.
>>>>
>>>> -Dan
>>>>
>>>
>>>
>>> --
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>>> http://www.opera.com/mail/
>>>
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>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>
>
>
--
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Received on Wed Aug 15 2012 - 14:00:06 PDT
