[gmx-users] Does adding artificial mass cause problems for friction studies?

Dallas Warren dallas.warren at monash.edu
Tue Dec 11 00:17:41 CET 2018

Look into heavy hydrogens (x4 mass) which is one way to increase the time
step since the frequency of vibrations for the hydrogen bond is decreased
due to the increase in mass.  Should be a number of references out there
looking into the effect the mass increase has directly.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Tue, 11 Dec 2018 at 09:04, James <james at ryley.com> wrote:

> Hi,
> When studying friction it can be inconvenient for a structure to have low
> mass. If you push on the structure hard enough to overcome static friction,
> it then accelerates so rapidly that the speeds are unrealistic.
> One way to overcome this problem is to increase the structure's mass. But,
> adding many atoms increases simulation time. A work-around might be to
> artificially increase the masses of certain atoms. For example, tell
> GROMACS that H weighs 1,000 instead of 1.
> But, artificial masses raise a variety of questions about the accuracy of
> the results. I can't find anything on this in the literature. Does anyone
> know about this, or know of relevant studies?
> Sincerely,
> James Ryley
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