Re: veldcdfile command

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jun 29 2017 - 05:12:26 CDT

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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