I am currently running a simulation of NMA (ACE - NAD in oplsaa, ACE - NME in charmm). In order to reproduce previous work with charmm, I have followed the instructions scattered throughout the Gromacs website to get the simulation running. I have been able to perform:
constraint=
all-bonds
h-angles
all-angles
with charmm (1 NMA in 830 tip3p waters). They have not yet finished, so I cannot be sure of their correctness. With the same shell scripts, I ran the same system with the oplsaa force field. With this, I have been able to perform:
constraint=
all-bonds
h-angles
without errors, but the NMA blows up after only 2 steps into the energy minimization when attempting to run the constraint=all-angles. Does oplsaa require any special information in the topology file to convert to angle constraints? If so, how can I go about doing this? I have included portions of my files below. Feel free to request any other information that may be of help.
Thanks in advance,
Justin
The actual error message is as follows:
"Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 5 and 11 at distance 1.102 which is larger than the 1-4 table size 1.000 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"
The simulation does not crash, but the pdb files clearly indicate an exploding NMA.
The em.mdp file is as follows:
#------- Energy Minimization: em.mdp -------#
title = ${MOL}
cpp = /usr/bin/cpp
constraints = all-angles
dt = 0.001 ; ps !
nsteps = 10000
nstlist = 1
rlist = ${CUT}
rcoulomb = ${CUT}
coulombtype = PME
rvdw = ${CUT}
pme_order = 6
fourierspacing = 0.05
ewald_rtol = 1e-6
constraint_algorithm = shake
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
_________________________________________________________________
Justin M. Shorb Phone: (608) 262-0483
Skinner Group [EMAIL PROTECTED]
University of Wisconsin-Madison, Department of Chemistry
1101 University Ave., Madison, WI, 53706
_______________________________________________ gmx-users mailing list [email protected] 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
