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

[Dr. Vitaly Chaban]

But you have conf.gro


On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth <katesedate at gmail.com> wrote:

> Well I am not getting the trajectory. Simulation crashes before any step
> is calculated :(
>
>
> On 5 April 2013 11:20, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>
>>
>>
>>> My problem is NVT crashes at step 0 and no energies or any other output
>>> file is written...
>>>
>>>
>>>
>> What about visualizing your interface?
>>
>>
>>
>>
>>
>>
>>
>>
>>> On 5 April 2013 10:25, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>>>
>>>> > 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 ***
>>>> >
>>>>
>>>>
>>>>
>>>>  Hmmm. Is it not easier to get surface tension from bulk simulation??
>>>>
>>>> On your error, I believe you broke some bond when extending your box in
>>>> Z
>>>> direction. Check energies at step 0 to be completely sure.
>>>>
>>>> Dr. Vitaly Chaban
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>>>
>>>
>>
>