From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Mon Jan 25 2016 - 12:31:10 CST
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
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
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