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 same
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 run
than reuse of the same random seed in a restart for langevin dynamics.
Regards - Bob Duke
----- Original Message -----
From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
To: <bill.mercury.chem.pitt.edu>; "AMBER Mailing List" <amber.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.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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Received on Wed Feb 11 2009 - 01:08:36 PST
