[gmx-users] Fwd: LJ cut-offs

[Thomas Piggot]

PS is the one type of lipid that doesn't work all that well in the 
CHARMM36 force field, even with the reparameterisation of the ion 
interactions that was done.

I'd be tempted to go with a difference force field unless there is a 
real reason for needing CHARMM36. Slipids, for example, should be fine 
for PS.

Cheers

Tom

On 11/01/17 18:57, Mohsen Ramezanpour wrote:
> Thanks Justin,
>
> Good to know. I used version 5.0 as Lee et al. 2015.
>
> I agree with you in general about keeping cut-offs the same.
>
> My systems are pure PS lipid membranes.
>
> The study by Klauda in 2016 shows that the higher order in PS membranes
> might be because of PS-PS or PS-K+ interactions.
> However, this was not done in Gromacs.
> This order was intensified when I used Gromacs (version 5.0, though). I
> will do with 5.1.* to see how it improves (hope it works).
>
>
> If PS-PS and PS-K+ interactions are not well defined, which results in
> higher order parameters, what would be a good solution for it?
> 1) reparameterization of PS lipids
> 2) reparameterization of PS-cationic ions interactions
> 3) possibly changing the cut-offs, say, 8-10 A.
>
> What do you think for this specific case (PS lipids)?
>
> Thanks
>
>
> On Wed, Jan 11, 2017 at 11:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/11/17 12:46 PM, Mohsen Ramezanpour wrote:
>>
>>> Hi Guys,
>>>
>>> Thanks for your comments. My question was exactly what Dawid clarified.
>>> Sure, I will read those as you suggested.
>>>
>>> Dawid, regarding this:
>>> "You need to keep in mind however that each force field was optimized for
>>> given set of cut-offs and
>>> they virtually become part of that FF (just like FF formula and
>>> parameters), so it is strongly recommended
>>> not to change them"
>>>
>>> I agree. BUT, using charmm36 in gromacs or other software requires to
>>> change some critical parameters like cut-offs to get a better agreements
>>> with experiments as well as with simulations done with charmm/NAMD.
>>> This is why.
>>>
>>>
>> As of version GROMACS 5.1, after which a small bug in force-switching was
>> fixed (see the link that Tom posted), this should not be true.  The
>> settings listed in the GROMACS website for CHARMM36 should correctly
>> reproduce what people do in NAMD or CHARMM using the same cutoffs.  We did
>> a lot of work to make sure this was the case.  Cutoffs are a function of
>> the force field, not the software.
>>
>> For a pure membrane, there is a valid comparison to be made between
>> 0.8/1.2 and 1.0/1.2 switching as Tom has noted, but for a membrane protein
>> 1.0/1.2 is what you should use (and from data I have collected and seen,
>> the differences between the two switching ranges are small, in any case).
>>
>> -Justin
>>
>>
>> Cheers
>>> Mohsen
>>>
>>> On Wed, Jan 11, 2017 at 5:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>> On 1/10/17 10:40 PM, Mohsen Ramezanpour wrote:
>>>>
>>>> Dear gromacs users,
>>>>> Please let me know your opinion on the following question:
>>>>> Thanks in advance for your comments
>>>>>
>>>>>
>>>>> dx.doi.org/10.1002/jcc.21287
>>>> While that paper (obviously) focuses on CHARMM, there is a vast amount of
>>>> general MD information described in it, as well as cited literature.  The
>>>> section on nonbonded interactions probably addresses most of what you
>>>> want
>>>> to know.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> ---------- Forwarded message ----------
>>>>> From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
>>>>> Date: Thu, Jan 5, 2017 at 5:20 PM
>>>>> Subject: LJ cut-offs
>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>>>
>>>>>
>>>>> Dear Gromacs users,
>>>>>
>>>>> Every force field has been parametrized with a specific LJ cut-off which
>>>>> must be the same for simulations using that force field.
>>>>> However, I was wondering if there is any reason why people usually take
>>>>> even numbers (e.g. 8-10, 8-12, 10-12 all with a difference of 2) for LJ
>>>>> cut-offs in force field development?
>>>>> Is there any rule that prohibit the use of 9-10, 9-11, or 11-12 for LJ
>>>>> cut-off?
>>>>>
>>>>> Thanks
>>>>>
>>>>> Cheers
>>>>> Mohsen
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>

-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.