Hi,
A patch that fixes this issue is now live (AT12 bugfix.21). It will be
applied when you re-run configure and recompile. Let me know if there
are any more problems.
-Dan
On Wed, Aug 15, 2012 at 2:33 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> 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
>>>>>
>>>>
>>>>
>>>> --
>>>> 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)
>>
>>
>>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Fri Aug 17 2012 - 07:00:03 PDT
