Dear Amberites
I am doing a GPCR membrane simulation.
After stepwise minimization of my system, I did a 20ps NVT
simulation from
0-100 K followed by an NPT simulation of 100 ps from
100-300K.
Everything looked okay until 20ps NVT simulation (to 100K).
However, when I
applied NPT conditions and raised temp to 300K, the
inner/outer water layers
got displaced.
My last 100ps NPT input file is as follows:
----------------------------------------------------------------------------
Angi Apo in DMPC Water Ions: Second 100ps NPT Equilibration
MD with harmonic
rest on Protein backbone: Heat from 100-300 K
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
ntp = 2,
pres0 = 1.0,
taup = 2.0,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 100.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
restraint_wt=10.0
restraintmask=':1-297.CA,C,O,N,H'
/
--------------------------------------------------------------------------
My questions are:
Q.1 Is this displacement of water,protein (system) normal? I
mean I
understand that applying NPT conditions will adjust the
volume of cell to
increase or decrease?
Q.2 I am using ntb = 2, ntp = 2, pres0 = 1.0,
taup = 2.0
2.A. Since I am simulating a membrane protein, and my BOX is
RECTILINEAR (as
mentioned in OUT file), I considered using ntp = 2 which is
anisotropic
pressure scaling? I want to confirm if it makes sense or
shall I use ntp =
1?
2.B. In addition, I used taup = 2.0. In the mannual it says
that deafult
value is 1.0 but higher values might be necessary if
trajectories are
unstable. What should be the reasonable value of this
parameter to be used
in membrane protein simulation.
2.C. Pressure/time graph also suggests that during last 100
ps, pressure has not be stabalized around 1 atm. What can I
do to to take care of this issue?
Q.3. Is harmonic restraint of 10.0 too low, shall I increase
it to 50.0 or
something?
I will be great help if you can provide me some suggestions
to solve these
problems.
Thanks and Best Regards
Akshay
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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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Received on Sun Feb 11 2007 - 06:07:11 PST
