From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jun 29 2017 - 07:11:45 CDT
Laura:
please try this new patch.
Jerome
On 29 June 2017 at 12:12, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Well, I tried to see if a quick hack would be sufficient. Looks like it
> isn't.
>
> On 28 June 2017 at 21:26, Laura Joana <laurajoanalopes_at_gmail.com> wrote:
>
>> I just forgot to say that this is the first time NAMD tries to write into
>> the veldcd file after the name was changed !
>>
>> On Wed, Jun 28, 2017 at 9:25 PM, Laura Joana <laurajoanalopes_at_gmail.com>
>> wrote:
>>
>>> Hello Giacomo,
>>>
>>> I saw this just after I sent my last e-mail. So I tried that and I got *Bad
>>> file descriptor* just after *WRITING VELOCITIES TO DCD FILE AT STEP 220*,
>>> when NAMD tries to write in the veldcd file.
>>> Bests,
>>>
>>> Laura
>>>
>>> On Wed, Jun 28, 2017 at 8:36 PM, Giacomo Fiorin <
>>> giacomo.fiorin_at_gmail.com> wrote:
>>>
>>>> Hi Laura, I think Jérôme has inadvertently made a diff against a source
>>>> tree used for testing Colvars before integration with NAMD, hence the
>>>> inconsistent Makefile.
>>>>
>>>> You can simply use the same patch without the segments affecting the
>>>> Makefile, as attached.
>>>>
>>>> Giacomo
>>>>
>>>> On Wed, Jun 28, 2017 at 2:09 PM, Laura Joana <laurajoanalopes_at_gmail.com
>>>> > wrote:
>>>>
>>>>> Thanks Jérôme !
>>>>> But I'm getting an error in the compilation:
>>>>> *No rule to make target `src/colvarproxy.C', needed by
>>>>> `obj/colvarproxy.o'. Stop.*
>>>>>
>>>>> On Wed, Jun 28, 2017 at 6:41 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>>>> wrote:
>>>>>
>>>>>> Sorry, try this patch instead.
>>>>>>
>>>>>> On 28 June 2017 at 18:05, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>>>>>>
>>>>>>> Hi Laura,
>>>>>>>
>>>>>>> Indeed, DCDfile seems to be getting special treatment. Please apply
>>>>>>> the attached patch to the source, rebuild NAMD and see if it helps.
>>>>>>>
>>>>>>> Jerome
>>>>>>>
>>>>>>>
>>>>>>> On 28 June 2017 at 16:59, Laura Joana <laurajoanalopes_at_gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear users,
>>>>>>>>
>>>>>>>> I'm having an issue using the veldcdfile command. I need to change
>>>>>>>> the veldcd file name after some MD steps and apparently this is not
>>>>>>>> possible My error message is just:
>>>>>>>> *FATAL ERROR: Setting parameter veldcdfile from script failed!*
>>>>>>>> I tried to do the same with the dcdfile command and it works. So it
>>>>>>>> seems that these two commands do not behave in the same manner. If someone
>>>>>>>> can explain to me why and/or has a solution for my problem I'll be happy !
>>>>>>>> I got this error message from namd versions 2.11 and 2.12, both
>>>>>>>> compiled from source code.
>>>>>>>> Thank you all,
>>>>>>>>
>>>>>>>> Laura
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Giacomo Fiorin
>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>> Contractor, National Institutes of Health, Bethesda, MD
>>>> http://goo.gl/Q3TBQU
>>>> https://github.com/giacomofiorin
>>>>
>>>
>>>
>>
>
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