[gmx-users] surface tension-crash at step 0

[Elisabeth]

Hi all,

I have problem ruunning NVT with Z direction extended to get surface
tension of a polymer packed in a cell. I tried the same procedure for an
alkane and NVT works well however for the polymer the run crashes at the
very first step..

Doe anyone have clue what wrong could be? Many thanks.

starting mdrun 'Polymer'
10000000 steps,  10000.0 ps.
step 0
[node6:14338] *** Process received signal ***
[node6:14339] *** Process received signal ***
[node6:14338] Signal: Segmentation fault (11)
[node6:14338] Signal code: Address not mapped (1)
[node6:14338] Failing at address: 0x2aaaafbbaca0
[node6:14339] Signal: Segmentation fault (11)
[node6:14339] Signal code: Address not mapped (1)
[node6:14339] Failing at address: 0x2aaaafbbd2e0
[node6:14339] [ 0] /lib64/libpthread.so.0 [0x3112e0ebe0]
[node6:14339] [ 1] /usr/local/gromacs/lib/libgmx_mpi.so.6 [0x2b2fd8203c54]
[node6:14339] *** End of error message ***
[node6:14338] [ 0] /lib64/libpthread.so.0 [0x3112e0ebe0]
[node6:14338] [ 1] /usr/local/gromacs/lib/libgmx_mpi.so.6 [0x2b4b10e86c65]
[node6:14338] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 14338 on node node6 exited on
signal 11 (Segmentation fault).



On 4 April 2013 12:59, André Farias de Moura <moura at ufscar.br> wrote:

> just that simple: as soon as you expand the box in the z direction the
> systems releases the excess pressure by the expansion of the liquid into
> the evacuated region.
>
>
> On Thu, Apr 4, 2013 at 1:20 PM, Elisabeth <katesedate at gmail.com> wrote:
>
>> Dear Dr. Moura,
>>
>> Thank you for your answer. I equilibrated the cell under NPT and then
>> extended the Z direction to get a surface. Since I run NVT and Z is
>> extended, I see no pressure dependence and surface tension values are
>> similar for all P from 50 to 1000 bar. which is attributed to the fact that
>> Z is extended and system tends to expand regardless of the pressure that
>> was imposed in the initial NPT runs. I have no gas, it is liqiuid-vaccum
>> and wanted to know if there is anyway to capture effect of pressure. From
>> your answer I think there is no such possibility...
>>
>> Please comment if the answer is positive,
>> Thank you
>>
>>
>>
>> On 4 April 2013 10:32, André Farias de Moura <moura at ufscar.br> wrote:
>>
>>> There's no simple answer for that. If you apply a lateral pressure (xy
>>> plane) and the system is evacuated in the z direction, the only thing
>>> that
>>> you might expect is that your system would be squeezed in that direction,
>>> and then the lateral pressure would relax.
>>>
>>> If you're thinking about a gas exerting a pressure on the interface, your
>>> system would need to have a pressurized gas instead of vacuum in the z
>>> direction. Please note that pressure would arise from the gas you have
>>> put
>>> into the box and not from an external pressure bath (I would stick to NVT
>>> for such a model). Among the possible issue you might face, the gas would
>>> probably be partially miscible in the liquid phase for high pressures.
>>>
>>> I hope it helps.
>>>
>>> cheers
>>>
>>> Andre
>>>
>>>
>>> On Wed, Apr 3, 2013 at 11:07 PM, Elisabeth <katesedate at gmail.com> wrote:
>>>
>>> > Hello all,
>>> >
>>> > Does anyone know how one can study the effect of pressure on surface
>>> > tension of pure liquids?
>>> >
>>> > Thanks,
>>> > --
>>> > gmx-users mailing list    gmx-users at gromacs.org
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>>> >
>>> >
>>>
>>>
>>> --
>>> _____________
>>>
>>> Prof. Dr. André Farias de Moura
>>> Department of Chemistry
>>> Federal University of São Carlos
>>> São Carlos - Brazil
>>> phone: +55-16-3351-8090
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>
>>
>
>
> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
>