AMBER Archive (2009)
Subject: Re: [AMBER] Stability of a long NPT md trajectory?
From: Bill K (bill_at_mercury.chem.pitt.edu)
Date: Mon Feb 09 2009 - 14:56:53 CST
Thank you for the kind replies to my inquiry. I found your
messages to be confusing initially until I realized my egregious
mistake in applying the ibelly flag. I should have instead put in
my input file (to freeze residue 1):
Belly Residues (dynamic residues)
RES 2 xxxx
For edification purposes, though, I found that using ntt=3
and not setting an ig value is what allowed the density to go
such a high value.
Thank you again for your time.
> There may be a number of things going on here relating to nonstandard
> approach to md, but one thing I noticed immediately is the use of ntt = 3.
> This in itself is not a problem, but one must be certain to not use the
> random seed at each restart - you must set a new value for "ig", and I
> didn't notice it in the sample mdin. I don't understand at all why your
> density would be so high though - there is much more abnormal about this
> than reuse of the same random seed in a restart for langevin dynamics.
> Regards - Bob Duke
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
> To: <bill_at_mercury.chem.pitt.edu>; "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Monday, February 09, 2009 7:08 AM
> Subject: Re: [AMBER] Stability of a long NPT md trajectory?
>> this should not happen.
>> however, I suspect something related to your use of the belly option
>> for nearly everything in the system. sander should have printed a
>> warning about use of ibelly with pme- take a look at that. you may
>> want to use resrtaints instead, but it's hard to give advice when we
>> don't know why you defined only 1 dynamic residue.
>> On Mon, Feb 9, 2009 at 2:07 AM, Bill K <bill_at_mercury.chem.pitt.edu>
>>> 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 =
>>> 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 =
>>> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS
>>> EELEC = -71680.3923 EHBOND = 0.0000 RESTRAINT =
>>> EKCMT = 0.2890 VIRIAL = 636.5491 VOLUME =
>>> Density =
>>> 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
>>> carry on production runs at either NVT, or NVE with ntb=1 and ntt=0),
>>> 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
>>> # 1ns Dynamic Simulation with Constant Pressure
>>> # Control section
>>> 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,
>>> type = 'TEMP0', istep1 = 1, istep2 = 999999, value1 = 300.0, value2 =
>>> Belly Residues (dynamic residues)
>>> RES 1
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