[gmx-users] rlist, rcolumb, and rvdw

[Thomas Piggot]

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.

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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>

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