From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jan 25 2016 - 12:23:01 CST
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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