Re: RATTLE failure

From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Sun Sep 09 2007 - 13:41:47 CDT

I will try this, but at the moment my simulation is running fine after
160ps (so
about 10 times as long as previously) now I have unfixed the atoms. I suspect
the fixed atoms were messing around with the SHAKE/RATTLE/SETTLE (whatever is
used) on the hydrogens attached to glycine residues since I had the backbone
fixed. Fingers crossed for the full .5 ns I asked for!!!

Philip Peartree

Quoting Himanshu Khandelia <hkhandel_at_memphys.sdu.dk>:

> Philip,
>
> In my personal experience, there are problems with the way SHAKE has been
> implemented in NAMD. When I use SHAKE and use a 2 fs timestep, there is
> significant drift in the simulation.
>
> In CHARMM, shake is well implemented, but I would recommend you to stay
> away from it in NAMD, especially if you have an anisotropic system like a
> lipid bilayer. Stick to a 1fs time step, and use 2 and 4 for nonbondedfreq
> and fullelectfrequency.
>
> Hope this helps,
>
> -himanshu
>
> ----------------------------
> Himanshu Khandelia, PhD
> Research Assistant Professor (Postdoc)
> MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
> University of Southern Denmark (SDU)
> Campusvej 55,
> Odense M 5230, Denmark
>
> Phone: +45 6550 3510
> Fax: +45 6550 4048
> email: hkhandel_at_memphys.sdu.dk
> WWW: www.memphys.sdu.dk/~hkhandel
> -----------------------------
>
>
> On Sat, 8 Sep 2007, Philip Peartree wrote:
>
>> 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
>> > > > >
>> > > > >
>> > > >
>> > >
>> > >
>> > >
>> > >
>> >
>>
>>
>>
>>
>
>

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