From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jan 25 2016 - 12:47:00 CST
If nothing changes, it means the issue is not linked with ABF or the
colvars.
Can you send me (off-list) a complete config file and log file for your
latest test?
Jerome
On 25 January 2016 at 19:31, Azadeh Alavi <azade.alavi_at_gmail.com> wrote:
>
> Dear Jerome
>
> Thank you so much again. I tried both approaches but nothing changed.
>
> Best regards,
> Azadeh
>
> On Mon, Jan 25, 2016 at 9:53 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> To help with troubleshooting, can you please try these with NAMD 2.11:
>>
>> - same simulation where you keep the colvars on but remove the abf block;
>> - same simulation, without colvars (colvars off).
>>
>> Thanks,
>> Jerome
>>
>> On 25 January 2016 at 19:11, Azadeh Alavi <azade.alavi_at_gmail.com> wrote:
>>
>>> Dear Jerome
>>>
>>> Thank you very much again. I tried version 2.11 and the nightly build
>>> but they still give the error except that these lines are added:
>>>
>>> TCL: Running for 1000000 steps
>>>
>>> ETITLE: TS BOND ANGLE DIHED
>>> IMPRP ELECT VDW BOUNDARY
>>> MISC KINETIC TOTAL TEMP
>>> POTENTIAL TOTAL3 TEMPAVG PRESSURE
>>> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>>>
>>> ENERGY: 0 8062.6566 35646.8483 27534.9645
>>> 755.5399 -346883.3941 74472.9707 118.9229
>>> 0.0000 nan nan nan
>>> -200291.4912 nan nan nan
>>> nan 1227471.4718 nan nan
>>>
>>>
>>> The fact is that I have done the ABF simulations before without any
>>> problem. The problem raised when I mutated one ion, taking care of all the
>>> input files.
>>>
>>> Best regards,
>>> Azadeh
>>>
>>> On Mon, Jan 25, 2016 at 8:38 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>> wrote:
>>>
>>>> Can you try version 2.11? The binaries are available for download. If
>>>> that still gives the error, please try the nightly build, just in case, and
>>>> let us know.
>>>>
>>>> Best,
>>>> Jerome
>>>>
>>>> On 25 January 2016 at 18:00, Azadeh Alavi <azade.alavi_at_gmail.com>
>>>> wrote:
>>>>
>>>>>
>>>>> Dear Jerome
>>>>>
>>>>> Thank you very much for your reply. I am using NAMD 2.10 for
>>>>> Linux-x86_64-multicore, and version 2014-10-23 of colvar.
>>>>>
>>>>> Best regards,
>>>>> Azadeh
>>>>>
>>>>> On Mon, Jan 25, 2016 at 5:44 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>>>> wrote:
>>>>>
>>>>>> Hi Azadeh,
>>>>>>
>>>>>> What version of NAMD and colvars are you using?
>>>>>>
>>>>>> Best,
>>>>>> Jerome
>>>>>>
>>>>>> On 25 January 2016 at 14:58, Azadeh Alavi <azade.alavi_at_gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Dear NAMD users
>>>>>>>
>>>>>>> I am performing MD simulations of a membrane-protein system. The
>>>>>>> problem is that in my ABF simulations, the run stops with the segmentation
>>>>>>> fault. I do not have the memory problem.
>>>>>>>
>>>>>>> The last few lines of the .log file are as below:
>>>>>>>
>>>>>>> Info: useSync: 1 useProxySync: 0
>>>>>>> Info: Startup phase 10 took 0.0123789 s, 1217.61 MB of memory in use
>>>>>>> Info: Startup phase 11 took 0.000143051 s, 1217.61 MB of memory in
>>>>>>> use
>>>>>>> Info: Startup phase 12 took 0.000791073 s, 1217.83 MB of memory in
>>>>>>> use
>>>>>>> Info: Finished startup at 22.5293 s, 1217.83 MB of memory in use
>>>>>>>
>>>>>>> TCL: Running for 1000000 steps
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Thank you very much for your help.
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Azadeh
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:09 CST