Re: [AMBER-Developers] hydrogen mass repartitioning

From: Adrian Roitberg <>
Date: Wed, 12 Mar 2014 17:52:24 -0400

I agree that Parmed should be the canonical way to repartition.

We (my group) will not distribute our own version of the repartitioning
script and in fact, have moved to using Parmed for that. Jason and I
have previously checked that Parmed indeed does what is supposed to do.


On 3/12/14 4:45 PM, Jason Swails wrote:
> How is everybody doing the mass repartitioning? ParmEd? Their own
> scripts? AFAIK ParmEd is the only way that is documented, implemented, and
> included in the upcoming release. If I'm wrong somebody please correct me.
> I don't know that ParmEd has worked its way into many peoples' standard
> workflows so I'm not comfortable assuming everybody's using it to
> repartition masses.
> If people are using their own scripts to do this repartitioning I think it
> is worth comparing against the "reference" implementation (preferably what
> we're pushing on users) to make sure everybody's doing the same thing...
> On Wed, Mar 12, 2014 at 3:23 PM, Carlos Simmerling <
>> wrote:
>> our not-very-extensive study shows that all of the thermodynamic
>> distributions that we've measured are within precision for 4fs vs 2fs, but
>> there is notably greater tendency to crash in high T parts of REMD at 4fs.
>> On Wed, Mar 12, 2014 at 3:17 PM, David A Case <
>>> wrote:
>>> On Wed, Mar 12, 2014, Adrian Roitberg wrote:
>>>> 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.
>>> So, is the final "a." your initial, or your choice between the two
>>> alternatives listed above?
>>> Further, the "it works" might be true in a thermodynamic sense
>> (==correctly
>>> samples the Botzmann distrbution), or might also be true in a kinetic
>> sense
>>> (==rates of hopping among basins is roughly unchanged as well).
>>> ...dac
>>> _______________________________________________
>>> AMBER-Developers mailing list
>> _______________________________________________
>> AMBER-Developers mailing list

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
AMBER-Developers mailing list
Received on Wed Mar 12 2014 - 15:00:04 PDT
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