[gmx-users] mdrun error

Hector Mrz-Seara Monne hseara at netscape.net
Sat Oct 2 13:39:10 CEST 2004

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:

       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)

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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