From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Wed Jun 28 2017 - 14:26:17 CDT
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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