Re: veldcdfile command

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Fri Jun 30 2017 - 07:38:02 CDT

Hi Jérôme,
It works perfectly!!! Thank you!
Laura

On Thu, Jun 29, 2017 at 2:11 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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--001a114b750af76c9505532cb140--

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