AMBER Archive (2009)

Subject: [AMBER] Stability of a long NPT md trajectory?

From: Bill K (bill_at_mercury.chem.pitt.edu)
Date: Mon Feb 09 2009 - 01:07:24 CST

Hi Everyone,
    I'm running a relatively long (~10ns) trajectory of a single
solute in a water box of approx. 1000 tip3p waters, with standard
conditions of 300K and 1Atm. I apologize if this is an elementary
question, but I've been surfing the mail reflector for some time
now... I've brought the system to temperature
with NVT runs of at least 20ps (I've tried up to 1ns), and then
switched to NPT (using the input at the end of the message), with
ntt = 3. When I do this, I notice that, throughout the run, the
volume continues to decrease, and the pressure remains negative,
even after the system density surpasses 1 by a large margin.
the final output before the calculation crashes is:

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000

 NSTEP = 313500 TIME(PS) = 353.500 TEMP(K) = 569.51 PRESS = -3544.4
 Etot = -71984.1552 EKtot = 1.6976 EPtot = -71985.8528
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -305.4604
 EELEC = -71680.3923 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 0.2890 VIRIAL = 636.5491 VOLUME = 8314.1509
                                                    Density = 3.8796
 Ewald error estimate: 0.9533E+00

So, instead of trying to do production runs using NTP, should I stop
the NTP run when my density is in the range of (1 or just over), and then
carry on production runs at either NVT, or NVE with ntb=1 and ntt=0), or
should this run be self regulating and stable and I've just completely
missed something? I appreciate your time and consideration.
    thank you very much
     -Bill

# 1ns Dynamic Simulation with Constant Pressure

 # Control section
 &cntrl
  ntwx = 500, ntpr = 500,
  ntt = 3, gamma_ln = 1.0, temp0 = 300.0, tempi = 300.0, tautp = 1.0,
  scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
  ntb = 2, ntc = 2, ntf = 2,
  nstlim = 999999, dt = 0.0010,
  ntp = 1, taup = 5.0, pres0 = 1.0
  ibelly = 1, ntr = 0,
  imin = 0, irest = 0, ntx = 5, nmropt = 1,
 /
 &wt
  type = 'TEMP0', istep1 = 1, istep2 = 999999, value1 = 300.0, value2 =
300.0,
 /
 &wt
  type='END'
 /
Belly Residues (dynamic residues)
RES 1
END
END

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