From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Sat Sep 08 2007 - 15:41:20 CDT
I will try letting the simulation run free. In production I would do,
so I don't
see the harm. I did do minimisation before thermalising the enzyme. I believe
RATTLE is separate to the algorithm that fixes the atoms. I just wondered
whether the fixed nature of the atom might be causing the RATTLE algorithm (I
think I have settle on) to fail. Only one way to find out!!!
Philip Peartree
Quoting Eric Perim <eric.perim_at_gmail.com>:
> As far as I know constraining the backbone will only reduce de computational
> cost of the simulation, since it will reduce the degrees of freedom, but I
> guess a totally free equilibration will be at least as effective as this
> one, but surely more time consuming. If the structure was not subject to any
> kind of geometry optimization before the equilibration I guess it would be
> good to let it free.
> One important thing is that the RATTLE algorithm is used to keep the bonds
> rigid, I don't know if it is the same as the one used to keep the atoms
> fixed. If it is a different algorithm, then it may be worth a try to fix the
> atoms through the fixedatoms options, instead of making the bonds rigid.
>
> Eric
>
>
> On 07/09/2007, Philip Peartree <P.Peartree_at_postgrad.manchester.ac.uk> wrote:
>>
>> Thanks Eric, I had contemplated it! One thing I am wondering, atom
>> referenced in
>> the error is a backbond carbon (incidentally part of a glycine) and at
>> the time
>> I am running with fixed backbone.
>>
>> When I used to run in charmm (with the same sim) I used to constrain the
>> backbone when equilibrating and then release the backbone. Is there any
>> point
>> in either of these things or would a totally free equilibration be better?
>> Up
>> to this point I've heated to 300K (totally free) and equilibrated the
>> waterbox
>> (with the protein fixed)
>>
>> I reckon this might solve the error, as I have seen in other posts that
>> fixing
>> atoms introduces unreasonable forces into the system.
>>
>> Philip Peartree
>>
>> Quoting Eric Perim <eric.perim_at_gmail.com>:
>>
>> > Hi Philip,
>> >
>> > I got this error more than once, what I did to solve it was turn off the
>> > rigibonds option (left only the solvent rigid). It may not be the best
>> > solution but it works.
>> >
>> > Eric
>> >
>> >
>> > On 04/09/2007, Philip Peartree <P.Peartree_at_postgrad.manchester.ac.uk>
>> wrote:
>> >>
>> >> Hi All,
>> >>
>> >> I'm getting a "ERROR: Constraint failure in RATTLE algorithm" in my
>> >> simulations,
>> >> anyone know what could cause this? I read on the list that increasing
>> the
>> >> Margin parameter could help, so I set it at 1.0, would further
>> increases
>> >> help
>> >> or is it something more fundamental? My sim is a protein in an 80x70x80
>> >> water
>> >> box, with PME and this part of the simulation it fails in has the
>> backbone
>> >> atoms fixed but all others free? It happens after about 200ps.
>> Previously
>> >> (before setting the Margin parameter) it happened after about 30ps.
>> >>
>> >> Philip Peartree
>> >>
>> >>
>> >
>>
>>
>>
>>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:14 CST