From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Fri Sep 07 2007 - 16:43:57 CDT
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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