Re: segmentation fault in ABF simulations

From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Mon Jan 25 2016 - 12:11:58 CST

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