AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 09 2009 - 06:08:29 CST

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> wrote:
> 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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