On Mon, 10 Nov 2008 00:45:19 +0000
"andrea hanna" <[EMAIL PROTECTED]> wrote:
Dear users,
I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and
the following parameters (only a few are given):
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.002
nsteps = 125000
comm-mode = Linear
nstcomm = 1
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 1.0
domain-decomposition = no
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
epsilon-r = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.0
I recently noticed from the manual that the nstlist should be 5 with gromos
96 ff. I have a couple of questions.
1. should this be 5 with a 0.001 timestep or with a 0.002 timestep
2. As I have done a lot of work using these parameters I was really looking
for some suggestions/advice as to whether I can use any of my data - I;m
really clinging onto hope here! And as to how 'badly' this choice/mistake
will have affected my work.
The nstlist is one issue but the most worrying is the use of a straight
cutoff at 1.0 nm for the vdW. This should be 1.4 nm and makes a big
difference.
Note also that I am not sure this force field has not been tested for PME and
developed for Reaction-Field. You should check the original paper.
You can rerun some of your jobs with a parameter set closer to the original
and check whether your observable vary significantly or not. That is
probably the best you can do.
XAvier.
Thanks,
Les
-----------------------------------------------------
XAvier Periole - PhD
- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------
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