[gmx-users] Long range Lennard Jones

[Gianluca Interlandi]

Thanks for your replies, Mark. What do you think about the current 
DispCorr option in gromacs? Is it worth it trying it? Also, I wonder 
whether using DispCorr for LJ + PME for Cb justifies reducing the cutoff 
for non-bonded to 1 nm with the CHARMM force field, where 1.2 nm is 
usually recommended.

Gianluca

On Wed, 28 Aug 2013, Mark Abraham wrote:

> Secondarily, one could use the same cut-off for LJ and electrostatics,
> and treat their respective lattice components however you like. This
> simplifies implementations for computing short-ranged interactions,
> while facilitating iso-accuracy load balancing across heterogeneous
> compute units.
>
> Mark
>
> On Wed, Aug 28, 2013 at 10:08 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> On 2013-08-28 09:31, rajat desikan wrote:
>>>
>>> Hi,
>>> What is LJ PME? I googled it and got this publication?
>>> http://pubs.acs.org/doi/abs/10.1021/ct400146w
>>>
>>> So, LJ will not be cut off at some r, but you will have a real+fourier
>>> part
>>> similar to electrostatics. Is that LJ PME? What are the advantages?
>>>
>> http://pubs.acs.org/doi/abs/10.1021/ct400140n
>>
>>>
>>> On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham
>>> <mark.j.abraham at gmail.com>wrote:
>>>
>>>> Lennard-Jones PME is planned for 5.0
>>>>
>>>> Mark
>>>> On Aug 28, 2013 8:36 AM, "Gianluca Interlandi"
>>>> <gianluca at u.washington.edu>
>>>> wrote:
>>>>
>>>>> Hi!
>>>>>
>>>>> Just wondering whether gromacs has (or plans to implement) a correction
>>>>> for the loss of long range LJ interactons? Something similar to
>>>>> LJcorrection in NAMD or IPS in CHARMM.
>>>>>
>>>>> Thanks!
>>>>>
>>>>>       Gianluca
>>>>>
>>>>> ------------------------------**-----------------------
>>>>> Gianluca Interlandi, PhD gianluca at u.washington.edu
>>>>>                      +1 (206) 685 4435
>>>>>                      http://artemide.bioeng.**washington.edu/<
>>>>
>>>> http://artemide.bioeng.washington.edu/>
>>>>>
>>>>>
>>>>> Research Scientist at the Department of Bioengineering
>>>>> at the University of Washington, Seattle WA U.S.A.
>>>>>                      http://healthynaturalbaby.org
>>>>> ------------------------------**-----------------------
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>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
-----------------------------------------------------