[gmx-users] charmm36 ions fix

[Justin Lemkul]

On 6/20/16 1:36 PM, gromacs query wrote:
> My simulation cases are above 0.5 M (that is 500 mM) which are then higher
> than as mentioned 100mM. Sorry I could not get when you say "correct
> nonbonded settings". You mean vdW/electrostatic cutoff and switch/shift
> etc. If it is the case then yes as am following proper mdp file taken from
> some recent paper where they reproduce membrane properties but under normal
> physiological salt conc. And also am using default CHARMM36 nonbonding
> pairs with nbfix. Is there anything more to be considered?
>

Check and make sure:

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

> So am wondering what should be done as I need to use above 0.5 M salt in
> membrane-protein simulations.
>

Follow the analysis of the Venable paper to see if you're seeing any spurious 
interactions.  Perhaps what you're seeing is actually real, but if it's at odds 
with experimental data, then it's probably not (depending on the quality of the 
experimental data).

-Justin

> Thanks for any suggestions.
> JIomm
>
> On Mon, Jun 20, 2016 at 6:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>
>> ==================================================
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>> Gromacs Users mailing list
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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

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