[gmx-users] UREA + Protein Simulation error.

[karan syal]

Dear Gromacs users,

I am trying to run a urea+protein simulation and encountering a few problems
at various stages.

I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I
started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K)

I am using this equilibrated box to add to a globular protein of about 250
residues using following commands :


editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron    (Giving me
a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the
number of urea above box should add is 2448.)

genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro   (*This adds 2064
Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M
urea box i have solvated with??)*


When i try to minimize this using the following em.mdp


cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  steep
nsteps              =  5000
coulombtype = PME
pme_order = 4
nstlist = 5
ns_type = grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
;       Energy minimizing stuff
;
emtol               =  100
emstep              =  0.01


*It gives me the following output*


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =         5000
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is
larger than the 1-4 table size 2.000 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
or with user tables increase the table size

t = 0.015 ps: Water molecule starting at atom 34477 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -1.3092671e+22
Maximum force     =            inf on atom 12598
Norm of force     =            inf

gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)



*When i look at the file in VMD, the protein is completely out of the box +
There are unusual bonds between a lot of UREA and SOL molecules*. ( The
unusual bonds are artifcats after minimization which are not there when i
initially look at my P48_10Mrea.gro, that is the gro generated after genbox
wth -cs as 10M urea)

I tried constraining hbonds as well in em.mdp bit to no effect.


I used the above em.gro to run a production run, with following pr.mdp


cpp = /usr/bin/cpp
define = -DPOSRES
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100000 ; total 200 ps
nstcomm = 1
nstxtcout = 50 ; collect data every 1 ps
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 100
nstenergy = 100
nstlist = 5
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl = V-rescale
tau_t = 0.1 0.1 ; use items in bold if you have Cl ions
tcgrps = Protein Non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 1
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529




*the simulation stops after following error*

t = 0.002 ps: Water molecule starting at atom 36943 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates




Can anyone pls suggest what should i modify to effectively simulate my
system?



Any suggestions regarding how i can run a urea+protein simulation with the
exact desired concentration will be highly appreciated.




Thanks for all the time and pateince,
Regards
Karan
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