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
>>>
>>
>>
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> 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)
--
-------------------------
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 - 13:30:02 PDT
