[gmx-users] charmm36 ions fix

[Justin Lemkul]

On 6/20/16 1:19 PM, gromacs query wrote:
> Thanks Justin, basically am stuck with an old question of using high salt
> conc. with membrane simulations and their dependence on force field
> parameters versus experiments. Membrane thickness and area seems to be
> sensitive to high salt at least in simulations.
>

Define "high."  The paper that derived and validated the lipid-ion NBFIX terms 
only used up to 100 mM, so if you're going much beyond that, there may be issues 
that need additional work.  The NBFIXes were validated using osmotic pressure at 
much higher concentration, but membranes are, of course, somewhat unique 
environments.

You're using the correct nonbonded settings, right?  The C36 lipids are very 
sensitive to misuse...

-Justin

> JIom
>
> On Mon, Jun 20, 2016 at 5:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/20/16 12:30 PM, gromacs query wrote:
>>
>>> Hi All,
>>>
>>> I am using charmm36 downloaded from (MacKerell website). Somehow I was
>>> enlightened while reading some papers applying NBFIX by Roux et al. I can
>>> see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
>>> default (via forcefield.itp) but the file does not mention any reference
>>> where it comes from. I read the doc file but could not find reference
>>> (sorry if missed it) or may be am missing the developmental stages thus it
>>> became quite a obvious thing. I am just wondering if nbfix.itp indeed
>>> comes
>>> from Roux et al.
>>>
>>>
>> We don't (really, can't possibly) provide all the references for all the
>> parameters in the C36 port.  That would require parsing all the comments in
>> all of the CHARMM force field files.  Those are also freely available and
>> are the definitive source of all this information.
>>
>> I assume you're referring to the SOD-CLA NBFIX?  That is indeed from Luo
>> and Roux JPCL 2010 (osmotic pressure calculations).  The same goes for
>> POT-CLA.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================