[gmx-users] rlist, rcolumb, and rvdw
jalemkul at vt.edu
Wed Jan 11 13:51:31 CET 2017
On 1/11/17 2:57 AM, Mark Abraham wrote:
> 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
To emphasize, this is especially true for CHARMM lipid parameters, as is the
Repeat after me: "I will not mess around with cutoffs for lipids." :)
> On Wed, 11 Jan 2017 04:51 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
>> Dear gromacs users,
>> Reading through mailing list I found a nice discussion on the relation
>> between rlist, rcolumb, and rvdw:
>> If I understood correctly,
>> rcoulomb < rlist and rvdw < rlist is the most accurate way,
>> 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
>> *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
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