[gmx-users] Fwd: LJ cut-offs

[Mohsen Ramezanpour]

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
>>>
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>>>
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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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