[gmx-users] Fwd: LJ cut-offs

[Mohsen Ramezanpour]

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
>>
>> ==================================================
>>
>> --
>> 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.
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



-- 
*Rewards work better than punishment ...*