From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Mon Jul 03 2017 - 06:13:06 CDT
Hello!
I'm having the same problem with the xstfile command now. I tried to look
what Jérôme did for veldcdfile, but I'm not familiar with the code, so I
could not find a solution to my problem.
Can someone help me (maybe still Jérôme) ?
Bests,
Laura
On Fri, Jun 30, 2017 at 2:38 PM, Laura Joana <laurajoanalopes_at_gmail.com>
wrote:
> 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.
>>>>>>>>>
>>>>>>>>> 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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