[gmx-users] All-bonds vs. H-bonds using CHARMM36

[rajat desikan]

Thank you, Justin!
I did intend to use h-bonds for the CHARMM36 simulations and all-bonds
elsewhere (depending on the FF). I just wanted some clarity before I
proceeded.


On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/31/13 2:21 PM, rajat desikan wrote:
>
>> Hi,
>> In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds
>> are constrained for the lipid simulations using SHAKE (excerpt from the
>> paper below)
>>
>> "Consistent for all of these simulations was the use of a 1 fs time step
>> and constraining of the hydrogen atoms using the SHAKE algorithm."
>>
>> For a membrane-protein system, is constraining all-bonds via LINCS the
>> right option while using CHARMM36?
>>
>>
> Normally, as the paper states, only bonds involving H are constrained with
> CHARMM.  LINCS is a suitable replacement for SHAKE, though you can use
> SHAKE in Gromacs if you want.  LINCS is generally more robust.
>
>
>  There was a mention somewhere (I forgot) that constraining all-bonds
>> probably prevents alkane isomerisations in membranes, which could lower
>> the
>> melting temperature. I intend to simulate a POPC bilayer. Can someone with
>> experience please shed some light on this?
>>
>>
> Can't comment on this, but I doubt there is any issue if you don't
> constrain all bonds.
>
>
>  P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on
>> lipidbook. Their .mdp constrains h-bonds
>> http://lipidbook.bioch.ox.ac.**uk/uploads/package/CHARMM36/**
>> 48-POPE-wurl/v1/charmm_npt.mdp<http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp>
>>
>>
> It is very uncommon that such input files exist without specifically
> requesting them; if this is exactly what the authors used, I see no reason
> to deviate from it unless you have a demonstrably superior protocol.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore