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

[Elisabeth]

The structure is taken from the end of previous simulation which terminates
successfully. The initial structure should not be the problem. What I do
only edit the last line (Z direction) of this structure to create vacuum.

This the output from log file.

Charge group distribution at step 0: 81 188 161 159 158 57 72 84
Grid: 3 x 3 x 6 cells
Initial temperature: 425.057 K

Started mdrun on node 0 Fri Apr  5 17:16:37 2013

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
    5.40484e+03    8.26652e+03    2.54277e+03    1.31894e+03   -6.08804e+02
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
    8.31491e+05    1.40229e+03    8.49817e+05    4.04825e+09    4.04910e+09
  Conserved En.    Temperature Pressure (bar)
    4.04910e+09    1.12122e+08    7.78980e+08

and here is the output.log from the previous run (bulk simulation)

DD  step 19998999  vol min/aver 0.918  load imb.: force  2.0%

           Step           Time         Lambda
       19999000    19999.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
    5.39477e+03    8.19320e+03    2.63606e+03    1.32991e+03   -5.94134e+02
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
   -4.34831e+03    1.34243e+03    1.39539e+04    1.52157e+04    2.91697e+04
    Temperature Pressure (bar)
    4.21421e+02    5.21511e+02

DD  step 19999999  vol min/aver 0.866  load imb.: force  1.0%

           Step           Time         Lambda
       20000000    20000.00000        0.00000

Writing checkpoint, step 20000000 at Sat Mar  9 22:16:02 2013


   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
    5.29484e+03    8.23267e+03    2.54182e+03    1.31784e+03   -6.08717e+02
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
   -4.35248e+03    1.37024e+03    1.37962e+04    1.55820e+04    2.93782e+04
    Temperature Pressure (bar)
    4.31565e+02   -9.33582e+02

    <======  ###############  ==>
    <====  A V E R A G E S  ====>
    <==  ###############  ======>

    Statistics over 20000001 steps using 2000001 frames

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
    5.25008e+03    8.19447e+03    2.71542e+03    1.36750e+03   -5.69335e+02
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
   -4.29465e+03    1.31685e+03    1.39803e+04    1.53404e+04    2.93207e+04
    Temperature Pressure (bar)
    4.24873e+02    1.57552e-01







On 5 April 2013 16:34, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:

> 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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>>>>>
>>>>
>>>>
>>>
>>
>