Hi
Well, first, tell us if you are going to increase or decrease the masses...
This has a long history in the field, and for the most part, it has
never worked well.
Basically, there are arguments about lowering masses to increase
diffusion coefficients. This seems ok, but then all vibrational
frequencies go up and you need a much short time step to make it work.
Hence, no gain.
You can increase all masses, and then you get to increase your time
step. That seems reasonable, but simple stats mech will show you that
what you have messed up with the velocities. If you are still running at
the same temperature as before, let's say 300K, that correlates with the
kinetic energy. So, if your kinetic energy is the same as with regular
masses, your velocities must have been reduced as the square root of the
mass change. So, things will move slower, and you loose...
There is something called HMR, hydrogen mass repartitioning. We are
about to submit a paper on this, but essentially consists of taking
local chemistry (e.g. CH2RR')
and increasing the H mass and decreasing the H-partner mass in such a
way that the 'local' mass has not changed.
This means that the total mass of the system is still the same as before
the repartitioning, and things are much better from a stat mech point of
view.
Once you do this, you can push your time step to 4 fs and gain a factor
of 2x in overall speed.
This is an EXPERT mode... We tested it a lot in amber, with different
observables, and it work great. Some other people within Amber have also
tried it and it works for them. Again, things break sometimes, so the
use does not come with a warranty...
Some of these ideas were expressed in "Improving efficiency of large
time-scale MD simulations in hydrogen rich systems. Feenstra, Hess,
Berendsen. J Comp Chem 1999"
On 5/13/14 10:59 AM, Brian Radak wrote:
> I don't think this kind of "trick" has been used in AMBER very often, if at
> all. Most classical static quantities of interest in the canonical ensemble
> are mass invariant, so your plan is likely sound, but I don't have any
> ideas as to how sampling will be affected. Perhaps that is why it is not
> done very often?
>
> Regards,
> Brian
>
>
> On Tue, May 13, 2014 at 10:51 AM, Manikanthan Bhavaraju <
> manikanthanbhavaraju.gmail.com> wrote:
>
>> Dear All,
>>
>> I am interested to study the mechanism of protein aggregation using an
>> explicit solvent simulations. As a model system we have taken a amyloid
>> protein ~ 100 residues. Initially, I would like to analyze the affect of
>> scaling of atomic mass of the water molecules vs. standard simulation
>> techniques. My assumption is that scaling the atomic mass of the solvent
>> molecules can decrease the viscosity of the system, avoid heating
>> (performing minimization and production runs), take larger time steps, and
>> the system to some extent will be able to quickly cross the energy barriers
>> on the potential energy surface.
>>
>> On the other hand, I want to conduct a regular explicit solvent simulation
>> (minimization, heating, equilibration, and production) and then compare
>> both the results. Can you anyone give me some suggestions or their expert
>> opinion on this kind of analysis?
>>
>> Thanks,
>>
>> mani
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
--
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 Tue May 13 2014 - 10:00:02 PDT
