Yang Ye, I just can't understand why the program ran fine in one way, but crashed in another way. If the two coordinates file are the same, how come did the second run give me large value of LJ_14? If it is possible, I can give you my two tpr file, you can do the test.
I used a coarse grained model, dt = 0.002. I don't think it is too large for a monomer. By the way, it seems David has not told us how to input multiple tablep.xvg files, right? All the best! Dongsheng On Fri, 2006-07-14 at 12:49 +0800, Yang Ye wrote: > reduce timestep or further minimization/equilibration? > > Yang Ye > > Dongsheng Zhang wrote: > > Dear GMX users, > > > > > > I have a coarse-grained model whose nonbonded potentials are tabulated, > > so I have to use user defined potential in gromacs. With Yang Ye's great > > help, I can implement the new force field. However, the program always > > crashed because of Large VCM(group rest). I have done a test by run the > > program in two different ways. My new force field uses gromos FF format, > > so I used c6 and c12 parameters. > > > > > > First I ran the program in a normal way, which means I use LJ for > > regular VDWs and 1-4 interactions. The program ran fine. > > > > Second I copied table6-12.xvg to my working directory and rename it to a > > proper name, then I used this table as my user-defined potential for > > VDWs and 1-4 interactions. > > > > I expect the above two ways give me very similar results. This is true > > for the first 51 steps. In step 52, the second run suddenly crashed > > because of Large VCM(group rest). > > > > The details are as following: > > > > The differences in two mdp files: > > > > 59c59 > > < vdw-type = user ;cut-off > > --- > > > >> vdw-type = cut-off; user ;cut-off > >> > > > > The information from two log files: > > > > full2.log (first run): > > > > Step Time Lambda > > 51 0.10200 0.00000 > > > > Energies (kJ/mol) > > Bond Angle LJ-14 Coulomb-14 LJ > > (SR) > > 3.02207e+02 3.00007e+02 -3.73112e+01 0.00000e+00 -2.27638e > > +02 > > Coulomb (SR) Potential Kinetic En. Total Energy > > Temperature > > 0.00000e+00 3.37264e+02 1.01670e+03 1.35397e+03 3.09963e > > +02 > > Pressure (bar) > > 4.78614e+00 > > > > Step Time Lambda > > 52 0.10400 0.00000 > > > > Energies (kJ/mol) > > Bond Angle LJ-14 Coulomb-14 LJ > > (SR) > > 3.00485e+02 2.99534e+02 -3.73372e+01 0.00000e+00 -2.27861e > > +02 > > Coulomb (SR) Potential Kinetic En. Total Energy > > Temperature > > 0.00000e+00 3.34820e+02 1.01849e+03 1.35331e+03 3.10508e > > +02 > > Pressure (bar) > > 4.73457e+00 > > > > Step Time Lambda > > 53 0.10600 0.00000 > > > > Energies (kJ/mol) > > Bond Angle LJ-14 Coulomb-14 LJ > > (SR) > > 2.98871e+02 2.99071e+02 -3.73627e+01 0.00000e+00 -2.28077e > > +02 > > Coulomb (SR) Potential Kinetic En. Total Energy > > Temperature > > 0.00000e+00 3.32503e+02 1.02011e+03 1.35262e+03 3.11004e > > +02 > > Pressure (bar) > > 4.67219e+00 > > > > > > > > > > full.log (second run): > > > > Step Time Lambda > > 51 0.10200 0.00000 > > > > Energies (kJ/mol) > > Bond Angle LJ-14 Coulomb-14 LJ > > (SR) > > 3.02206e+02 3.00007e+02 -3.73112e+01 0.00000e+00 -2.27636e > > +02 > > Coulomb (SR) Potential Kinetic En. Total Energy > > Temperature > > 0.00000e+00 3.37266e+02 1.01670e+03 1.35397e+03 3.09963e > > +02 > > Pressure (bar) > > 4.78604e+00 > > > > Step Time Lambda > > 52 0.10400 0.00000 > > > > Large VCM(group rest): -362781422043267072.00000, > > 46998104838242304.00000, -95810352322707456.00000, ekin-cm: inf > > Energies (kJ/mol) > > Bond Angle LJ-14 Coulomb-14 LJ > > (SR) > > 3.00484e+02 2.99534e+02 -9.09769e+31 0.00000e+00 -2.27860e > > +02 > > Coulomb (SR) Potential Kinetic En. Total Energy > > Temperature > > 0.00000e+00 -9.09769e+31 inf inf > > inf > > Pressure (bar) > > inf > > > > Step Time Lambda > > 53 0.10600 0.00000 > > > > > > Compare step 51 in two cases, every item has very similar value. In step > > 52, the second run give me very large value of LJ14. This causes the > > problem. However I compare the output xtc files at step 52 i those twp > > runs. They are identical. It really surprises me that LJ-14 is so large > > in the second run. > > > > > > Any suggest to find what's wrong will be highly appreciated. If you need > > more information, please let me know. > > > > All the best! > > > > Dongsheng > > > > > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
