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 <vvcha...@gmail.com> wrote:
> But you have conf.gro
>
>
> On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth <katesed...@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 <vvcha...@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 <vvcha...@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
>>>>> --
>>>>> gmx-users mailing list gmx-users@gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at
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>>>>>
>>>>
>>>>
>>>
>>
>
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