OK,
thanks !
Best wishes,
Marek
Dne Fri, 17 Aug 2012 15:58:21 +0200 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> 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/
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
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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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>> http://www.opera.com/mail/
>>
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>
>
>
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Received on Fri Aug 17 2012 - 07:30:05 PDT
