[gmx-users] mdrun running without simulating new steps

[yan gao]

Hi Justin,

I think it is the minimization issue. I did steep for 2000 steps, and it 
works thereafter for the mdrun, for this structure.
Thank you very much!

Regards,
Stone Gao

--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Tuesday, September 01, 2009 4:35 PM
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] mdrun running without simulating new steps

>
>
> st wrote:
>> Hi,
>>  I run a two-molecule system with mdrun_d in a water box (~10000 water 
>> molecules.)
>> The program looks running properly (no errors nor warnnings)
>> However the program seems stop outputting files (because the output file 
>> size stop increases) after about 5min.
>> The mdrun_d interface looks normal without any errors, the md.log 
>> contains only two saves:
>
> <snip>
>
>> Grid: 9 x 9 x 14 cells
>>    Energies (kJ/mol)
>>            Bond          Morse          Angle       G96Angle    Proper 
>> Dih.
>>     3.35232e+05    3.27635e+01    7.09937e+02    1.73811e+01 
>> 2.47097e+03
>>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic 
>> En.
>>     1.48669e+05   -4.50390e+05   -1.89304e+04    1.78117e+04 
>> 4.38796e+05
>>    Total Energy  Conserved En.    Temperature Pressure (bar)
>>     4.56608e+05    4.56608e+05    1.09892e+03   -5.74950e+04
>>  Step           Time         Lambda
>>             100        0.05000        0.00000
>>  Energies (kJ/mol)
>>            Bond          Morse          Angle       G96Angle    Proper 
>> Dih.
>>     3.38536e+05    1.06967e+03    2.21584e+04    4.26526e+01 
>> 3.13457e+03
>>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic 
>> En.
>>     8.73487e+04   -5.64854e+05   -4.48577e+04   -1.57422e+05 
>> 3.56524e+05
>>    Total Energy  Conserved En.    Temperature Pressure (bar)
>>     1.99102e+05    7.60608e+05    8.92881e+02    7.56563e+04
>>
>
> I'd say the system is exploding.  Your temperature is oscillating between 
> 1000 K and 893 K using a Nose-Hoover thermostat, and your potential starts 
> off in excess of 10^4 kJ mol^-1.  Did you run any sort of energy 
> minimization or weak-coupling equilibration before this run?
>
> It's odd that mdrun wouldn't give some sort of LINCS warning or write out 
> step*.pdb files right beforehand, though.
>
> -Justin
>
>>  **********************
>>  ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>