[EMAIL PROTECTED] 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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