Hi all,
When simulating proteins in explicit solvent, I noticed that after a
while water molecules start "boiling off" the protein. The result is a
large and diffuse solvent cloud that becomes apparent after 5-10 ns of
simulated time.
First, I noticed it in some of my runs, but then exactly the same
problem appears to be present in one of the tutorial simulations
(
http://ambermd.org/tutorials/advanced/tutorial3/section2.htm). If you
download the resulting trajectory and display water, the solvent shell
starts evaporating after a couple of nanoseconds.
After I run a simulation for 20 ns with these parameters, the solute
remains completely solvent-free and all water boils off into space. Just
for the sake of completeness, I'm giving below the input files for all
stages of my simulation.
While the tutorial example uses somewhat different input, the solvent
behavior is the same.
Any thoughts would be very much appreciated.
Thank you
Sasha
Input files:
initial minimisation solvent
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 1,
ntr = 1,
cut = 15
/
Hold the protein fixed
500.0
RES 1 242
END
END
initial minimisation whole system
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 1,
ntr = 0,
cut = 15
/
Equilibration
protein: 20ps MD
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 15,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.001,
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep protein fixed with weak restraints
10.0
RES 1 242
END
END
Production MD
Production simulation
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 15, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 250000, dt = 0.001,
ntpr = 500, ntwx = 500, ntwr = 1000
/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 05 2008 - 14:34:44 PST
