AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Feb 09 2009 - 22:20:57 CST

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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER_at_ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER_at_ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER_at_ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER_at_ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber