On 2/27/13 10:25 AM, jesmin jahan wrote:
Thanks Justin.
Well, I am felling stupid now! Could you kindly provide me some better
.mdp parameters that make more sense?
gromacs 4.6 gives me error with my previous parameters which were
working perfect in gromacs 4.5.3
It says we have to use cut-off verlet, either we have to use coupling
temp or we have to set verlet-buffer-drift = -1.
Then it says set pbc to xyz or xy. I tried to change my rlist or other
cutoff values. It says box is too large or small.
So, i am really very confused!
It will be very kind of you, if you can suggest me some parameters
which match best with my previous parameters namely:
constraints = none
integrator = md
pbc = no
dt = 0.001
nsteps = 0
rcoulomb = 300
rvdw = 300
rlist = 300
nstgbradii = 300
rgbradii = 300
implicit_solvent = GBSA
gb_algorithm = HCT ;
sa_algorithm = None
gb_dielectric_offset = 0.02
optimize_fft = yes
energygrps = protein
-----------------------------
For implicit runs, I always set:
pbc = no
ns_type = simple
comm-mode = angular
rlist = 0
rcoulomb = 0
rvdw = 0
nstlist = 0
rgbradii = 0
nstgbradii = 1
coulombtype = cutoff
vdwtype = cutoff
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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