[gmx-users] NMA, oplsaa, charmm, constraints

Justin M. Shorb shorb at wisc.edu
Thu Aug 24 22:59:50 CEST 2006


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:


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:


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,

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				shorb at wisc.edu
University of Wisconsin-Madison,  Department of Chemistry
1101 University Ave., Madison, WI, 53706
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