[gmx-users] rlist, rcolumb, and rvdw

[Justin Lemkul]

On 1/11/17 9:42 AM, Thomas Piggot wrote:
> Well, IMHO, for a lipids only system I'd would actually change those to use
> rvdw-switch = 0.8. Not only is this consistent with the original CHARMM36 lipids
> publication but for DPPC/POPC (at least) produces better membrane properties in
> GROMACS.
>
> See https://github.com/NMRLipids/NmrLipidsCholXray/issues/4 and my
> comments/results in the discussion for more details.
>

Interesting discussion.  Indeed, the 1.0/1.2 cutoff settings are preferred for 
compatibility with everything in the CHARMM36 force field.  In our hands, when 
we tested DPPC, 0.8/1.2 and 1.0/1.2 produced results in reasonable agreement 
(e.g. the CHARMM-GUI paper referenced several times in that discussion) though 
compressibility increased with the shorter switching region.  We tested 0.8/1.0 
because everyone complains about the "long" cutoff required to use CHARMM :)  If 
only everything were like AMBER, which uses 0.8...

All of this should become moot as we work to refine the force field with the 
recently implemented dispersion PME.  No promises on when that will be done, of 
course.

-Justin

> Cheers
>
> Tom
>
> On 11/01/17 12:51, Justin Lemkul wrote:
>>
>>
>> On 1/11/17 2:57 AM, Mark Abraham wrote:
>>> Hi,
>>>
>>> Those ancient comments pertain only to the deprecated "group" cutoff
>>> scheme. You should look at the extensive documentation of both schemes in
>>> the current reference manuals. Particularly vdw cutoffs are baked into the
>>> forcefield and should not be varied without extensive testing. See
>>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>>>
>>
>> To emphasize, this is especially true for CHARMM lipid parameters, as is the
>> case here.
>>
>> Repeat after me: "I will not mess around with cutoffs for lipids." :)
>>
>> -Justin
>>
>>> Mark
>>>
>>> On Wed, 11 Jan 2017 04:51 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
>>> wrote:
>>>
>>>> Dear gromacs users,
>>>>
>>>> Reading through mailing list I found a nice discussion on the relation
>>>> between rlist, rcolumb, and rvdw:
>>>>
>>>> https://www.mail-archive.com/gmx-users@gromacs.org/msg08387.html
>>>>
>>>>
>>>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058507.html
>>>>
>>>>
>>>> If I understood correctly,
>>>>
>>>> rcoulomb < rlist and rvdw < rlist is the most accurate way,
>>>>
>>>> and
>>>> rlist=rcoulomb=rvdw is the commonly used way for these parameters.
>>>>
>>>> I was wondering what would be the case if I want to change the cut-offs?
>>>>
>>>> For instance, to use charmm36 in Groamcs, it is recommended to use 1.0-1.2
>>>>
>>>> as the cut-off for LJ, and rlist=rcoulomb=rvdw
>>>>
>>>> However, this setting might not result in good behaviour for some
>>>> lipid bilayers.
>>>>
>>>> Therefore, I want to check if other cut-offs works better in gromacs.
>>>>
>>>> If I change "1.2 nm" to "A nm" for rvdw, do I need to change rcolumb and
>>>> rlist to A as well? i.e. rlist=rcolumb=rvdw=A?
>>>>
>>>> I am using following parameters already:
>>>>
>>>> cutoff-scheme           = Verlet
>>>> nstlist                       = 20
>>>> rlist                          = *1.2*
>>>> coulombtype             = *pme*
>>>> rcoulomb                  = *1.2*
>>>> vdwtype                   = Cut-off
>>>> vdw-modifier            = *Force-switch*
>>>> rvdw_switch             = *1.0*
>>>> rvdw                        = *1.2*
>>>>
>>>> Thanks in advance for your comments
>>>> Cheers
>>>> Mohsen
>>>> --
>>>> *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

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