[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

[Dawid das]

Dear All,

I would like to come back to this discussion with following question. What
if I need to use CHARMM22 FF
for protein in water box + counterions and I have a computational package
that does not support Verlet
algorithm for neighbour search but link cells (index cells) approach
instead?
To what extent do I violate the applicability of parameters that were
optimized based on a different algorithm?

Dawid

2017-05-21 0:30 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 5/20/17 8:28 AM, Dawid das wrote:
>
>> Hi Mark,
>>
>> Thank you. Actually I want to do some QM/MM calculations with CHARMM22 for
>> MM part
>> but not using GROMACS and not all things that are implemented in GROMACS
>> are available in my
>> QM/MM package. Nevertheless, I still want to gather as much data as
>> possible.
>>
>>
> CHARMM force fields do not use multi-atom charge groups.  Each atom is its
> own group, so the neighbor searching is really always atom-based.  So while
> the group and Verlet cutoff schemes are obviously not the same algorithms,
> with respect to the removal of charge groups, they are the same.
>
> -Justin
>
>
> Best wishes,
>> Dawid
>>
>> 2017-05-19 22:28 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>>
>> Hi,
>>>
>>> Historically that was how things were done. Nobody thinks it is a good
>>> idea
>>> any more. Use the Verlet scheme plus the recommendations for CHARMM
>>> forcefields in GROMACS and you'll be fine - charge groups are removed
>>> perforce.
>>>
>>> Mark
>>>
>>> On Fri, 19 May 2017 18:44 Dawid das <addiw7 at googlemail.com> wrote:
>>>
>>> Dear  Gromacs Users,
>>>>
>>>> I am a bit confused whether I shouldn't use charge
>>>> group-based cut-off for electrostatics when using CHARMM22.
>>>> If I shouldn't use it, what is the purpose of specification of charge
>>>> groups in
>>>> original CHARMM files?
>>>>
>>>> Best wishes,
>>>> Dawid
>>>> --
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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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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