I agree with Scott
When we started looking into this, my idea was that either
a. it breaks, so we say bad things about other programs
or
b. it works, so we gain a factor of 2 in speed..
a.
On 3/12/14 1:06 PM, Scott Le Grand wrote:
> OTOH if you guys find a conceptual hole in HMR, it would be extremely
> useful for smacking the guilty parties (cough GROMACS cough AceMD) that
> made adding it to AMBER a necessity with a spiked clue-by-4...
>
>
>
>
> On Wed, Mar 12, 2014 at 8:34 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> Hi all
>>
>> Please try it out! Make sure to use the proper scripts to get the new
>> masses, do not just increase time step to 4 fs !
>>
>> We are writing a paper on this and will share it with everyone when we
>> have a good draft.
>>
>> adrian
>>
>> On 3/12/14 9:55 AM, Thomas Cheatham wrote:
>>>>> Note AMBER 14 will also support hydrogen mass
>>>>> repartitioning so in principal you can run at 4fs time step.
>>>> How much to we really know about this option? I've been playing with
>> it for
>>> We have been running a DNA 18-mer and also a RNA tetranucleotide r(GACC)
>>> with h-mass repartitioning on the solute only and on everything. From
>>> initial analysis, conformational distributions appear fairly identical
>> for
>>> the r(GACC), however we still need to look at kinetics, water properties
>>> (viscosity should be higher), etc. When Christina, Ros and I get it
>>> further analyzed, I'll summarize to the dev list...
>>>
>>>> Blue Waters (say) to run lots of simulations at 1, 2 and 4 fs time
>> steps?
>>>> Has anyone compared 2 and 4 fs where both have the mass repartitioning?
>>> Ros/Christina, maybe we should fire up some more as per above. --tom
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>> --
>> Dr. Adrian E. Roitberg
>>
>> Colonel Allan R. and Margaret G. Crow Term Professor.
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
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>>
> _______________________________________________
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> AMBER-Developers.ambermd.org
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--
Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Mar 12 2014 - 11:00:03 PDT
