this issue was resolved by using the non-standard spce.itp provided by acpypi. But I have a little problem still running in double precision
Run this script up to the point of minimization and it works. grompp -f em.mdp -c Complex_b4em.pdb -p Complex.top -o em.tpr mdrun -v -deffnm em however...when I use double precision grompp_d -f em.mdp -c Complex_b4em.pdb -p Complex.top -o em.tpr mdrun_d -v -deffnm em Back Off! I just backed up em.log to ./#em.log.2# Getting Loaded... Reading file em.tpr, VERSION 4.0.5 (double precision) Loaded with Money Back Off! I just backed up em.trr to ./#em.trr.2# Back Off! I just backed up em.edr to ./#em.edr.2# Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+02 Number of steps = 200 F-max = inf on atom 3 F-Norm = inf ------------------------------------------------------- Program mdrun_d, VERSION 4.0.5 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 1540 ] ------------------------------------------------------- On Sun, Dec 6, 2009 at 7:43 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jack Shultz wrote: >> >> We have a workflow going, and I switched to double precision because >> of the LINCS issues. I got this error now with grompp. I don't think >> anything else is different other than double precision, but I included >> the logs for this. >> >> ------------------------------------------------------- >> Program grompp_d, VERSION 4.0.5 >> Source code file: toppush.c, line: 1273 >> >> Fatal error: >> [ file spce.itp, line 32 ]: >> Atom index (1) in bonds out of bounds (1-0). >> This probably means that you have inserted topology section "bonds" >> in a part belonging to a different molecule than you intended to. >> In that case move the "bonds" section to the right molecule. >> ------------------------------------------------------- >> > > Please see the following: > > http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds > > Particularly of interest is the section within about the AMBER force fields, > for which the default spc.itp is incompatible. > > -Justin > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
