AMBER Archive (2007)

Subject: RE: AMBER: Membrane Simulation: NPT Issues

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Mon Feb 12 2007 - 09:33:40 CST

 
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_at_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. NOTE: My 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_at_olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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