

AMBER Archive (2007)Subject: AMBER: Umbrella sampling From: Franck Vendeix (Franck_Vendeix_at_ncsu.edu)Date: Fri Feb 09 2007  08:37:35 CST
Dear Amber users,
I am a subscriber of the amber reflector mailing list and I sent this
 Original Message 
Dear Amber users,
I am trying to determine the delta_G of different types of base pairs by
On Step1: I minimized the water molecule and the counter ions (Na+) by
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb = 1,
ntr = 1,
cut = 10
/
Hold the base pair fixed
500.0
RES 1 2
END
END
Step2: the entire system (base pair + water + ions) is minimized
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 10
/
Step3: equilibration of the system from 0 to 300 K for 5ps. This MD is
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 5000, dt = 0.001
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep base pair fixed with weak restraints
10.0
RES 1 2
END
END
Step 4: Equilibration at 300 K of the system during 40 ps
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 2.0,
nstlim = 40000, dt = 0.001,
ntpr = 100, ntwx = 100, ntwr = 1000
/
The system effectively reached equilibrium at the end of this
My plan is to start the umbrella sampling simulation after the
My guess is if I want to skip the equilibrium step 4 I should use
Is it better to use the distance between the center of mass of each
An example of an MD simulation input file used for the umbrella sampling
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 2.0,
nstlim = 1000, dt = 0.0005,
ntpr = 100, ntwx = 100, ntwr = 100
/
&wt type=DUMPFREQ, istep1=10 /
&wt type=END /
DISANG=dist.RST
DUMPAVE=dist_vs_2
Where the dist.RST files contains:
# distance restraint between A C1 and U C1
&rst iat=11,44, r1=0., r2=2., r3=2., r4=20., rk2 = 20.,
rk3 = 20., /
I will use 20 windows with 100 points collected for each (2000 points in
Is there any optimal time to be used for umbrella sampling? If yes,
Which method should be used to choose the best rk2/rk3 values?
I thank you in advance for your replies.
Regards,
Franck

 
