Ramachandran G wrote:
Dear all,
I am trying to minimize a protein structure but i noticed
initially before it starts minimization, it gives warning
-------------------------------------
Warning: 1-4 interaction between 1434 and 1490 at distance 1.783 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
Using 10 BFGS correction steps.
F-max = 7.89523e+03 on atom 1185
F-Norm = 4.87025e+04
------------------------------
finally it converged to machine precision but not to the requested
precision Fmax < 1000. When i view final structure, it
looks the residues are sprayed out. The mdp file which i used for
minimization is
This .mdp does not match the above output.
------------------------------------------------------------------------------------
Title = protien test
cpp = /lib/cpp
;include = -I../top
define = -DFLEXIBLE
constraints = none
integrator = steep
nstcomm = 1
dt = 0.002 ; ps !
nsteps = 50000
nstlist = 10
ns_type = grid
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
vdwtype = shift
rvdw = 1.2
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
------------------------------------------------------------
This protein structure has been minimized using Charmm but in gromacs i
am having problem. Can anyone help me. Thank you.
There's so many things you might have done to it since leaving CHARMM
that it's scarcely material that it was minimized there. Check your
termini and the locations of your solvent molecules. It's impossible to
help you further without more detail of your preparation.
Mark
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