On 02/07/13 12:10, Justin Lemkul wrote:
On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent <
richard.broadben...@imperial.ac.uk> wrote:
Not sure exactly what merging together means, for visualisation I
generally use vmd as this supports gromacs files directly.
If I understand correctly (and the OP can clarify if I haven't), it sounds
like visualization of the average structure shows atoms overlapping one
another. One should not necessarily expect anything reasonable from an
average structure.
http://www.gromacs.org/Documentation/Terminology/Average_Structure
Your problem might be to do with, using rlist, rcoulomb, and rvdw set to 0
is not the standard way to do an infinite cut-off normally you set them to
-1 as in the manual.
I have never seen cutoffs set to -1. Is this a special trick in the code?
The OP's settings are correct for infinite cutoffs and use of all-vs-all
kernels.
Yes sorry that's my mistake I should never respond to the mailing list
before having my morning coffee. Infinite cutoffs are specified with
rlist=0 etc.
Sorry for the confusion.
Richard
Also the AMBER force field was parametrised with a cut-off it might,
depending on what you are trying to do, be advisable to use the cut-off
specified in the original papers and the wider literature for the AMBER
force field.
This is an important point, but finite cutoffs like those used in
explicit-solvent simulations (on the order of 1.0 nm) have, in my hands,
produced terrible results in an implicit environment (poor energy
conservation, loss of structure, etc). Longer cutoffs are generally
recommended, and I only ever use infinite cutoffs in implicit systems. It
is definitely worth some time doing validation of one's settings.
Richard
On 02/07/13 10:07, Shine A wrote:
Sir,
I did a 10 ns REMD simulation for a peptide, 8 replicas using
amber
force field.Then extracted pdb file from the trajectory and clustered
using
g_cluster. The I viewed the average structure of the cluster in pymol .But
here the atoms are merged togather.why it happends?Is there any problem
with my force field? My md.mdp file as follows.
RESHELIX ; -DFLEXIBLE -DPOSRES
constraints = none
integrator = md
dt = 0.001 ; ps
nsteps = 10000000 ; 10000 ps = 10 ns
nstcomm = 10
nstcalcenergy = 10
nstxout = 500 ; frequency to write coordinates to
output
trajectory
nstvout = 0 ; frequency to write velocities to output
trajectory; the last velocities are always written
nstfout = 0 ; frequency to write forces to output
trajectory
nstlog = 1000 ; frequency to write energies to log
file
nstenergy = 1000 ; frequency to write energies to edr
file
vdwtype = cut-off
coulombtype = cut-off
pbc = no
nstlist = 0
ns_type = simple
rlist = 0 ; this means all-vs-all (no cut-off),
which
gets expensive for bigger systems
rcoulomb = 0
rvdw = 0
comm-mode = angular
comm-grps = system
optimize_fft = yes
; V-rescale temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc_grps = system
ref_t = 376.32
; Pressure coupling is off
Pcoupl = no
; Generate velocites is on
gen_vel = yes
gen_temp = 270
This doesn't make much sense to me. If you're generating velocities, you
should be generating them for the target temperature. If not, your
thermostat has to do some funny things to get it back on track. With
V-rescale (or Berendsen, for that matter), you may not have an issue since
it relaxes quickly. Other thermostats will cause you grief.
-Justin
gen_seed = -1
;
; Implicit solvent
;
implicit_solvent = GBSA
gb_algorithm = Still ; HCT ; OBC
nstgbradii = 1
rgbradii = 0 ; [nm] Cut-off for the calculation of the
Born radii. Currently must be equal to rlist
gb_epsilon_solvent = 80 ; Dielectric constant for the implicit
solvent
; gb_saltconc = 0 ; Salt concentration for implicit
solvent models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension = -1
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