Re: Atoms moving too fast; simulation has become unstable

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Sep 21 2015 - 00:58:32 CDT

Hi Peter,

I tried these steps to locate the error. I obtained your topology and
parameter files and the pdb file given in tip-kit, tip4p-after1ns.pdb. I
generated the psf file using vmd psfgen plugin.

First I tried simulating with your configuration file, tip4p-example.namd.
The the simulation worked and structure was preserved.

Then I tried with my configuration file, there I did not include waterModel
tip4p. The simulation worked but, the position of the OM atom was changed.
(structure distorted)

With waterModel tip4 option. Simulation was all fine.

When we specify parameters and topology, is it necessary to put the
waterModel option to tip4p? What does it specifically do? Can't we do it
alone with topology and parameters?

Best regards,
Monika

On Fri, Sep 18, 2015 at 9:31 AM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> Hi Monika,
> Those force constants only matter during minimization. As long as you have
> rigidbonds water or all (and you MUST have one of these set if you're using
> a rigid water model), as soon as you start the actual run, the geometry
> will be kept rigid, so by definition the force constants here won't matter.
> However, namd figures out the water geometry from the top/par files, so if
> you don't have all of the angle terms, that by itself could cause problems.
> Best,
> Peter
>
>
> On Thu, Sep 17, 2015 at 11:58 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
>> Thank you for the reply.
>>
>> Sourav, after running constant pressure first, the simulation actually
>> worked but now after minimization, the structure is distorted.
>>
>> Peter, I actually referred to your files in this link. There is the
>> difference between the parameter files. In my parameter file, I put the
>> force constant for LP OH2 bond as zero but in your one there is a force
>> constant. And there is an additional angle force constant in your parameter
>> file. May be this is the reason for my structure to get distorted. But,
>> when we include these force constants, wouldn't there be an error in the
>> energy calculated? Is there a bond between LP and OH2 in tip4p model or we
>> define the bond just to preserve the shape of the molecule. May be my
>> understanding on the geometry of tip4p could be wrong.
>>
>> Best regards,
>> Monika
>>
>> On Fri, Sep 18, 2015 at 8:14 AM, Peter Freddolino <petefred_at_umich.edu>
>> wrote:
>>
>>> Your topology looked ok to me. See also
>>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/0322.html
>>> for examples.
>>> You might also post your config file.
>>> Best,
>>> Peter
>>>
>>>
>>> On Thu, Sep 17, 2015 at 5:42 AM, Monika Madhavi <monikamadhavi_at_gmail.com
>>> > wrote:
>>>
>>>> Dear all,
>>>>
>>>> Thanks for your time. Farzad by the model, are you referring to the pdb
>>>> or topology. I think my pdb is fine but I am not sure about the topology
>>>> whether I need to define some lone pairs. I tried with smaller time steps.
>>>> Still getting the same error.
>>>>
>>>> Peter, I tried with turning on tip4p water model in config file and
>>>> without. Both failed. Is there a specific way that I should define the lone
>>>> pairs?
>>>>
>>>> Regards,
>>>> Monika
>>>>
>>>> On Mon, Aug 31, 2015 at 7:00 PM, Peter Freddolino <petefred_at_umich.edu>
>>>> wrote:
>>>>
>>>>> Dear Monika,
>>>>> This may be a silly question, but did you turn on the tip4p water
>>>>> model in your config file?
>>>>> Best,
>>>>> Peter
>>>>>
>>>>> > On Aug 31, 2015, at 6:42 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
>>>>> wrote:
>>>>> >
>>>>> > Dear all,
>>>>> >
>>>>> > I want to simulate water dynamics using TIP4P water model. My
>>>>> simulation box contains only water. For this I created my own parameter and
>>>>> topology files based on data available on some references. But when I try
>>>>> to simulate, the minimization goes OK but when it starts to equilibrate, it
>>>>> says "Atoms moving too fast; simulation has become unstable" and stops.
>>>>> When I examined the last frame, it seems that the structure is distorted. I
>>>>> think it may be due to an error in topology and parameters. Could you
>>>>> please suggest what is the correct way of writing parameters and topology
>>>>> files for namd simulations?
>>>>> >
>>>>> > The used files are as follows.
>>>>> >
>>>>> > !parameter file for TIP4P water
>>>>> > !
>>>>> > BONDS
>>>>> > !atom type Kb b0
>>>>> > HW HW 0.000 1.5139
>>>>> > OW HW 450.000 0.9572
>>>>> > OW OM 0.000 0.1577
>>>>> > ANGLES
>>>>> > !atom type Ktheta Theta Kub S0
>>>>> > HW OW HW 55.00 104.52
>>>>> > HW OW OM 50.00 52.26
>>>>> > NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
>>>>> > cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
>>>>> > !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 -
>>>>> 2(Rmin,i,j/ri,j)**6]
>>>>> > !
>>>>> > !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
>>>>> > !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
>>>>> > !
>>>>> > !atom ignored epsilon Rmin/2 ignored eps,1-4
>>>>> Rmin/2,1-4
>>>>> > !
>>>>> > OW 0.000000 -0.155300 1.576825
>>>>> > HW 0.000000 0.000000 0.000000
>>>>> > OM 0.000000 0.000000 0.00000
>>>>> > END
>>>>> >
>>>>> >
>>>>> > !topology for TIP4P water
>>>>> > !
>>>>> > MASS 300 HW 1.00800
>>>>> > MASS 301 OW 15.99940
>>>>> > MASS 302 OM 0.00000
>>>>> >
>>>>> > RESI TP4P 0.000
>>>>> > GROUP
>>>>> > ATOM OW OW 0.0000
>>>>> > ATOM HW1 HW 0.5200
>>>>> > ATOM HW2 HW 0.5200
>>>>> > ATOM OM OM -1.0400
>>>>> > BOND OW HW1 OW HW2 OW OM
>>>>> > !HW1 HW2 !this bond needed for SHAKE but not in NAMD
>>>>> > ANGLE HW1 OW HW2 HW1 OW OM HW2 OW OM
>>>>> >
>>>>> > IC HW1 OW OM HW2 0.9572 52.26 180.00 119.50 0.8697
>>>>> > IC HW2 HW1 OW OM 1.5139 37.74 0.00 52.26 0.1577
>>>>> > ACCEPTOR OM
>>>>> > PATCHING FIRS NONE LAST NONE
>>>>> > END
>>>>> >
>>>>> > Thank you.
>>>>> > Monika
>>>>> > --
>>>>> > W.A.Monika Madhavi
>>>>> > Lecturer (Probation),
>>>>> > Department of Physics,
>>>>> > University of Colombo.
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> W.A.Monika Madhavi
>>>> Lecturer (Probation),
>>>> Department of Physics,
>>>> University of Colombo.
>>>>
>>>
>>>
>>
>>
>> --
>> W.A.Monika Madhavi
>> Lecturer (Probation),
>> Department of Physics,
>> University of Colombo.
>>
>
>

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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