[gmx-users] LINCS warnings

rama david ramadavidgroup at gmail.com
Mon Jun 11 12:34:33 CEST 2012

Hi  Justin, thank you for quick reply.
You are right I have practicle result, And I want to replicate them..

Thank you for your suggestion..

With Best Wishes,
Rama David

On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> On 6/11/12 6:23 AM, rama david wrote:
>> Hi Mark,
>> I did simulation of the same system in vacuum, and system behave the
>> normally,
>> So the instability  in the system is due to the spc Water model???
>> As per the link http://www.gromacs.org/**Documentation/Terminology/**
>> Blowing_Up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
> The water model is not the problem.  Your solvated system has clashes that
> cause instability.  In vacuo, your solute has greater freedom to shift
> around.
>  I think the source is (Please tell me is it right..?? or any else reason
>>  )
>> last option :
>> you have a single water molecule somewhere within the system that is
>> isolated
>> from the other water molecules.
>> How to find such water molecule and solve the problem??
> I think this is unlikely.  If you have any isolated waters, they might be
> sandwiched somewhere in your protein layers and should be easy to spot.
>  The best strategy is to use the output of EM to your advantage.  Look at
> the atom that had the highest force on it.  What is it near?  What might it
> be clashing with?  What if you run EM in vacuo, followed by solvation, and
> another round of EM?
> From your earlier description, it seems to me that the system has been
> constructed to replicate some known experimental spacing, but doing so does
> not guarantee that whatever peptide structure you are replicating will
> necessarily produce a sensible result, or one that is free from clashes.
>  Hence, you need to refine the model before continuing.
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