AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Feb 10 2009 - 07:40:55 CST

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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