From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Wed Jun 28 2017 - 14:25:35 CDT
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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