AMBER Archive (2009)

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

From: Bill K (bill_at_mercury.chem.pitt.edu)
Date: Tue Feb 10 2009 - 13:39:22 CST

Hi,
    This is beginning and endpoint of the same trajectory,
which seems very curious to me. I can attach the entire output
(and input files), and you can see the density increasing and volume
decreasing throughout the simulation. I'd think that the ewald
error is a reflection of the use of the belly option for almost
the entire simulation box.
   -Bill

> Okay, I am just curious about how the heck this all happened. I am
> presuming that you did some steps between this timestep and the ~350 psec
> timestep under conditions different than the one mdin you have shown us
> (with belly on all the solvent). This intervening period is what is
> interesting - how the heck did the solvent contract to somewhere between a
> quarter and a third of normal volume? - very aphysical. What I have
> objected to is that the whole deal is due to belly - belly should have
> fixed
> the solvent atoms at the current volume, and you would only have the res 1
> atom rattling around. I note that for all the steps you have shown, the
> ewald error estimate is very bad - this in itself indicates something
> anomalous about the setup.
> Regards - Bob
> ----- Original Message -----
> From: "Bill K" <bill_at_mercury.chem.pitt.edu>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Tuesday, February 10, 2009 2:37 AM
> Subject: Re: [AMBER] Stability of a long NPT md trajectory?
>
>
> To shed some light on your discussion here, the solute
> was just a single atom, and oddly enough this NPT md
> run started with a typical TIP3P density as you get using
> solvatebox, as I'll show with the initial stats from the output:
>
> NSTEP = 0 TIME(PS) = 40.000 TEMP(K) = 217.61 PRESS = -190.3
> Etot = -72887.4935 EKtot = 0.6487 EPtot = -72888.1421
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -54.6700
> EELEC = -72833.4721 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 0.6487 VIRIAL = 189.3043 VOLUME = 45924.9288
> Density = 0.7024
> Ewald error estimate: 0.9839E+00
>
> and terminated, as below, using the input parameters that I provided.
> Certainly, freezing all of the solute was unintentional.
>
>
>> Yes, I think we are in violent agreement here. Something sort of
>> strange,
>> but I suspect the setup as much as how belly is used. The unknown is
>> the
>> size of the solute and whether it is more than 1 residue. But here's
>> the
>> kicker. Only residue 1 moves (makes sense from the low kinetic energy;
>> don't know what I think about no bonded energy terms at all - must be a
>> rather simple solute). But the belly has the solvent completely frozen
>> from
>> the start. So assume the solute is small. Then look at the per atom
>> volume - comes out to 2.77 angstrom**3 per atom. That is consistent
>> with
>> the high density, and way low for water which would more typically be
>> around
>> 10 angstrom**3 per atom at density 1.0. Now, given the belly, the
>> system
>> solvent STARTED out this way... So I would guess a fairly bogus initial
>> setup held that way with a NVT box as well as the belly, and when you
>> switch
>> to NPT the belly still holds you there. How/why the water got stacked
>> this
>> tight in the initial config, I haven't a clue, but I don't see how it
>> could
>> be from solvating with the standard water boxes... The belly
>> effectively
>> takes all solvent-solvent interactions out of the direct force calcs,
>> which
>> is why the pressure/virial is completely bogus (so in addition to the
>> belly
>> zeroing any calc'd forces on the solvent, it also skips their direct
>> force
>> virial contribution).
>> Regards - Bob
>>
>> ----- Original Message -----
>> From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
>> To: "AMBER Mailing List" <amber_at_ambermd.org>
>> Sent: Monday, February 09, 2009 10:10 PM
>> Subject: Re: [AMBER] Stability of a long NPT md trajectory?
>>
>>
>>> Bob,
>>> I agree that random seed issues can be problematic, but I doubt it
>>> could
>>> ever be anything of the scale seen here. his density is 3 times
>>> normal,
>>> but
>>> for some reason the energy hasn't exploded and the pressure is too low!
>>> This
>>> isn't just correlation issues, or non-ergodicity or something like
>>> that,
>>> it
>>> is simply completely wrong at the most basic level. i bet it's the
>>> belly
>>> option.
>>> carlos
>>>
>>>
>>> On Mon, Feb 9, 2009 at 9:21 PM, Robert Duke <rduke_at_email.unc.edu>
>>> wrote:
>>>
>>>> I think this may be a really small unit cell (1000 waters - perhaps
>>>> too
>>>> small) with significant periodicity issues that then magnify the
>>>> problems
>>>> associated with usage of the same random seed through multiple
>>>> restarts
>>>> with
>>>> ntt 3, but I am also somewhat skeptical that this is the only problem.
>>>> For
>>>> one thing, I did not get any indication of how many restarts were done
>>>> with
>>>> the same seed - may have been none. I mentioned it purely because it
>>>> is
>>>> something that folks tend to overlook, and it can cause really bad
>>>> problems.
>>>> Regards - Bob
>>>>
>>>> ----- 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 7:56 PM
>>>>
>>>> Subject: Re: [AMBER] Stability of a long NPT md trajectory?
>>>>
>>>>
>>>> I disagree- I run frequently with ntt=3 and no ig value and have
>>>> never
>>>>> seen the problem you reported.
>>>>>
>>>>> are you sure that just changing ig and nothing else really solved it?
>>>>>
>>>>> beware of problems that go away without explanation- they often come
>>>>> back without explanation too.
>>>>>
>>>>> as I said in my last email, if you use PME, make sure you understand
>>>>> the limits of ibelly as compared to positional restraints, which
>>>>> think
>>>>> are far safer. problems with ibelly and PME, especially during
>>>>> equilibration, are well documented in the archives.
>>>>>
>>>>> On Mon, Feb 9, 2009 at 3:56 PM, Bill K <bill_at_mercury.chem.pitt.edu>
>>>>> wrote:
>>>>>
>>>>>> Gentlemen,
>>>>>> 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
>>>>>> END
>>>>>> END
>>>>>> 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.
>>>>>> -Bill
>>>>>>
>>>>>> 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_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>
>>>>>>>> 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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>>>>>>>>>
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