[gmx-users] temperature explosion in NVE ensemble
Alex Robertson
alexrson at stanford.edu
Fri Jun 24 22:42:25 CEST 2005
Hi
I am trying to run a NVE ensemble featuring a short peptide in tip3p
water. No matter what I do my total energy always starts climbing rapidly
until I end up with a lincs error. I have tried prequilibriating with P and
T coupling on,only constraining hbonds, minimizing the energy in advance,
shortening the timestep to .3 fs, using various radii for pme and cutoffs
and increasing the lincs_order. In all of these cases I still get all major
components of my energy increasing rapidly. I am just wondering if any more
experienced users have resolved similar problems in gromacs.
Here are the relevant parts of my mdp:
dt = 0.002 ; This is the step I
nsteps = 2600000 ; total 5.2 ns
comm_mode = Linear
nstcomm = 1
nstxout = 500
nstvout = 100
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10 ; I have tried lowering this to 5
ns_type = grid
pbc = xyz ; means yes
rlist = 2.2
rcoulomb = 2.5
coulombtype = Cut-off
epsilon_r = 1 ; Could this value be the problem?
vdwtype = Cut-off ;
rvdw = 2.5
constraints = all-bonds
constraint_algorithm = lincs
Thanks so much,
Alex Robertson
PS
One thing I noticed is that in the GMX321 the manual recommends setting
lincs_iter to 2 for NVE, but this option is not availible in GMX314. Is
there some way to get around this?
----------------------------------------------
Alex Robertson
Pande Lab
Department of Chemistry
Stanford University
650-387-4149
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