[gmx-users] Fwd: LJ cut-offs

[Justin Lemkul]

On 1/11/17 1:46 PM, Dawid das wrote:
> Since I join this discussion, this is perhaps a good moment to ask
> following questions.
> I use Gromacs 5.0.4 and the file.mdp options that I found here
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM , so:
>
> 1. The bug that was described here
> https://github.com/NMRLipids/NmrLipidsCholXray/issues/4
> does not apply to my case if I used only CPUs, LJ for vdW and PME for
> electrostatics but I did use
> default -tunepme (I guess it does not apply then as far as I understand the
> manual). I just want to
> make sure that my calculations are correct.
>

If you only used CPU then you should be fine.  The complete release notes 
provide more detail.

http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x

> 2. With the above setting in my *.log file there is line saying
>
> Changing nstlist from 10 to 25, rlist from 1.2 to 1.235
>
> and this is because verlet-buffer-tolerance sets the rlist. Is that OK?
>

Yes.

-Justin

> Dawid
>
> 2017-01-11 19:34 GMT+01:00 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
> :
>
>> I found these two links from other post of mine which might be useful for
>> this discussion too:
>>
>> People have used 11-12 switching range as well. So, if it works, there is
>> no restriction to not choose such numbers with 0.1 nm difference in
>> cutoffs.
>>
>> http://pubs.acs.org/doi/abs/10.1021/jp101759q
>>
>>
>> There is a great discussion which is relevant and better to read.
>>
>> https://github.com/NMRLipids/NmrLipidsCholXray/issues/4
>>
>> Cheers
>> Mohsen
>>
>> On Wed, Jan 11, 2017 at 10:46 AM, Mohsen Ramezanpour <
>> ramezanpour.mohsen at gmail.com> 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.
>>>
>>> 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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>>>
>>>
>>>
>>> --
>>> *Rewards work better than punishment ...*
>>>
>>
>>
>>
>> --
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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

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