[gmx-users] Re: LINCS with amber99SB ?

[Justin A. Lemkul]

Yun Shi wrote:
> Thank you for the reply. Just to clarify.
> 
> In the original gromos 53a6 paper, all bonds were constrained, while in 
> amber99sb paper only bonds involving H atoms were constrained. So as 
> long as I stick to the same groups of bonds constrained as in the 
> development of respective forcefields, it is always OK to use LINCS 
> rather than SHAKE, right?
> 

I've never had a problem with either approach.

> And for those bonds not constrained when using amber99sb force field, 
> would GROMACS automatically apply the harmonic bond stretching 
> functional form as specified in the [ bonds ] section of corresponding 
> .itp files?
> 

Correct.

-Justin

> Regards,
> 
> Yun
> 
> 
> Yun Shi wrote:
>  > Hi all,
>  >
>  > I want to do MD simulation with amber99SB force field, which I found
>  > originally developed using SHAKE algorithm to constrain all bonds
>  > involving hydrogen atoms. But it seems to me that SHAKE is still not
>  > supported with domain decomposition in GROMACS4.5.4, and we can only use
>  > LINCS for bond constraints if we want to run MD simulations in parallel.
>  >
>  > So what should I use in simulating with amber99SB in parallel? LINCS
>  > constraining allbonds? LINCS constraining hbonds only? Or just run with
>  > SHAKE in one node?
>  >
> 
> You should be able to use LINCS with either all-bonds or hbonds. 
>  Running your
> simulation in serial, even for a relatively small system, will likely be
> painfully slow.
> 
>  > I would be very grateful if someone could tell me the relative accuracy
>  > (or if they are all good enough) and computational costs of these
>  > options above.
>  >
> 
> Either should be fine.  LINCS is actually somewhat more stable than SHAKE.
> 
>  > And maybe I should ask this question in the developers mailing list, but
>  > would GROMACS support SHAKE in parallel in the near future, like in a
>  > 4.5.5 version?
>  >
> 
> There will not be any new features in 4.5.5, and the 4.6 list of new 
> features is
> already basically agreed upon.  Gromacs is undergoing major code changes 
> that
> limit the amount of new features that will come out soon.  You can file a
> feature request on redmine.gromacs.org <http://redmine.gromacs.org/>, 
> but do not expect to see any activity on
> the issue until probably version 5.0.
> 
> -Justin
> 
> --
> ==============================
> ==========
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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