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 - 20:21:31 CST

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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