From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Apr 01 2015 - 10:51:31 CDT
You can change the timestep in the middle of the simulation, there is
nothing theoretically wrong with this. This is no different than simply
having as a starting structure whatever you came up with from the first
simulation. You do, of course, need to be careful in your analysis if any
of the properties you are analyzing have time dependent units and you try
to analyze the whole merged simulation at once.
If you observed a difference, are you sure it is actually because of the
change in timestep, or is it just something that would have happened if you
had run the simulation longer regardless? Particularly, if you think the
ligand is moving to a lower energy position, you would expect that to
happen in any case.
If there is actually a discrepancy between two different timesteps (this is
very hard to pin down, because of the stochastic nature of simulations),
then the only sensible conclusion would be that the smaller timestep is the
more reliable. But really, you'd have to do a number of runs with these
different timesteps, but both having the same total simulation time, in
order to be at all convinced that there was a real difference.
I have seen several cases of increasing the timestep after initial rough
equilibration. The logic being that early on you may be populating some
high energy states as you get rid of odd structural configurations from
whatever structure you started with, and these are likely to cause
instabilities in the simulation at higher timesteps. Once things have
settled, you can go higher and try to get more information with less
computational time. The same idea applies to the use of pressure vs.
constant volume. Adding a barostat will slow down the simulation, so in
some cases it can be effective to use the barostat for some initial time
until the volume of the cell equilibrates (from whatever initial
deformities/voids were caused by the solvation algorithm), and then move to
In the end, I've found there are a lot of "best practices" for MD that you
can glean from reading the methods of articles or looking over tutorials
written by experienced researchers, but there seem to be few hard rules.
Probably the best test in most cases is to run the simulation multiple
times, and if the results are all similar and lead to the same conclusion,
that is a good sign.
On Wed, Apr 1, 2015 at 11:28 AM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
> Dear Experts,
> For a trial I performed a simulation, initially the time step 1 assigned
> in configuration file, with rigidbond all, further, after 50 ns I changed
> tilmestep to 1.5, some questions related to this:
> 1. The change in the tilmestep leads to change in structural orientation,
> understood as integration time step is bound by the fastest bond vibration
> 2. Is this changing in time step is correct or wrong in the middle of
> simulations, I changed to check the system behaviour, as in curiosity, i
> observed that the receptor-ligand interaction increased.
> 3. If change in time step provides relevant results, is it possible to use
> these changes in result output for further analysis.
> Therefore, my observation for this work is this, initially at time step 1
> less receptor-ligand interaction, but after increasing time step to 1.5
> lead to change interaction orientations. This approach is correct or wrong,
> if wrong, how to make it correct? Can we increase time step after some nano
> I tried to search the mailing list, but not able to find something relevant
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:46 CST