AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 09 2009 - 18:56:50 CST

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