From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Sep 17 2015 - 21:44:09 CDT
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.
>
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