karan syal wrote:
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??)*
No, it shouldn't. The protein occupies space within that volume, as well.
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)
"Out of the box" doesn't exist for a periodic system. The "bonds" you see are
also *not* generated by Gromacs, but are also just an artefact of visualization.
Bonds are not created or broken in molecular mechanics.
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
Don't, it's a waste of time. Never just plow ahead when something isn't
working. There is something unreasonable about the starting structure. Try
minimizing the protein in vacuo first, then add your urea and try EM again.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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