[gmx-users] mdrun error

[David]

On Sat, 2004-10-02 at 13:39, Hector Mrz-Seara Monne wrote:
> Hello All,
> 
> Maybe the question that follow has been posted before but I wasn't
> able to find it, then if anyone knows where just told me. My problem
> is that my monolayer system is working well, but after a 1.7 ns of
> dynamics with a step 1fs I get the following error:
> 
Have you stopped the center of mass motion? Sometimes it ahs to be done
per group (e.g. monolayer and water).
Also your temperature is 450 K. Do you have T coupling turned on?


>        Step           Time         Lambda
>         1731000     1731.00012        0.00000
>                                                                                                           
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih.  Improper Dih.         
> LJ-14
>     3.07715e+04    6.36605e+03    2.02562e+03    1.27192e+03   
> 2.39194e+04
>      Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb
> (SR)
>    -4.35088e+03   -4.18427e+04   -3.79469e+03   -2.96826e+02  
> -1.61672e+04
>    Coulomb (LR)      Potential    Kinetic En.   Total Energy   
> Temperature
>     3.08142e+02   -1.78960e+03    3.78781e+04    3.60885e+04   
> 4.50009e+02
>  Pressure (bar)
>    -4.24753e+02
>                                                                                                           
> Large VCM(group rest):      0.00172,     -0.00977,     -0.00129,
> ekin-cm:  4.46633e+00
> Large VCM(group rest):      0.00213,     -0.00449,      0.00016,
> ekin-cm:  1.10213e+00
> Large VCM(group rest):      0.00437,     -0.00540,     -0.00333,
> ekin-cm:  2.64588e+00
> There were 90 inconsistent shifts. Check your topology
> Large VCM(group rest):      0.00420,     -0.00470,     -0.00106,
> ekin-cm:  1.82364e+00
> 
> There is anyone that with that information have any idea of what is
> going on. I'm sorry but I can't understand this message. Check what of
> the topology file. My topology file was made by PRODRG and extended by
> me manually, The system are 255 monomers of 
> 8C's-benzene-N=N-benzene-O-3C's-COOH monom in vacum. If you need
> anything else just tell me. 
> 
> Thanks in advance.
> 
> Hector Martínez-Seara Monné 
> 
> Universidad Barcelona 
> Dpt. Química-Física 
>  
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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