[gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

[Justin A. Lemkul]

gportel at gwdg.de wrote:
> 
> Hi everyone,
> 
> I'm having problems running an md simulation (with gmx-4.0.2) using vsites
> and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
> seems to occur when the molecule crosses pbc, since the first sign of the
> simulation not working fine after ~3ns is
> 
> "
> Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is larger
> than the 1-4 table size 2.400 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> "
> 

This is a commonly reported problem.  See here:

http://wiki.gromacs.org/index.php/blowing_up

Also search the list archives; you will pull up several hundred posts describing 
the problems other users have faced and how they overcame them.

Other things that would be helpful to know if you are still having problems: 
What does your system contain?  Did it adequately minimize?  What kind of 
equilibration procedure did you perform?

<snip>

> Tcoupl                   = v-rescale
> tc_grps                  = system
> tau_t                    = 0.1
> ref_t                    = 300.00

Maybe you want "Protein Non-Protein" instead of "system" here?  But that's just 
general advice, without any knowledge of what's in your system.

-Justin

> Pcoupl                   = Berendsen
> Pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> constraints              = all-bonds
> constraint-algorithm     = Lincs
> lincs-order              =  6
> lincs-iter               = 2
> lincs-warnangle          = 30
> 
> 
> I've tried, perhaps naively, using both options for periodic_molecule with
> the same results.
> 
> I guess it's hard to tell what did go wrong, but perhaps somebody has an
> idea.. I thought of submitting a bugzilla, but maybe there are some more
> tests I could do to pin point the problem before. Any ideas?
> 
> 
> All the best,
> 
> 
> Guillem
> 
> Dr. Guillem Portella
> MMB - Institute for Research in Biomedicine
> Parc Cientific de Barcelona
> http://mmb.pcb.ub.es/~gportella
> 
> 
> 
> 
> 
> 
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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