[gmx-users] mdrun error
spoel at xray.bmc.uu.se
Sat Oct 2 14:12:52 CEST 2004
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.
> 3.07715e+04 6.36605e+03 2.02562e+03 1.27192e+03
> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb
> -4.35088e+03 -4.18427e+04 -3.79469e+03 -2.96826e+02
> Coulomb (LR) Potential Kinetic En. Total Energy
> 3.08142e+02 -1.78960e+03 3.78781e+04 3.60885e+04
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users