[gmx-users] time step & constrains

Vivek Raut vraut at CLEMSON.EDU
Tue Apr 13 21:48:01 CEST 2004

Does it mean that if you do not place any constraints on your system, as it 
is demonstrated in the Gromacs Demo, keeping 2fs time step is likely to 
cause some error in the simulation result, say , as compared to the results 
in time step is kept at 1fs??

I am simulating adsorption of protein on the biomaterial SAM surfaces. The 
SAM surfaces are locally designed as per GROMACs .rtp file specifications & 
on the terminal end group, Hydrogen atoms have been added to complete the 
valency ( for e.g., adding a H to make a -OH terminated surface). But these 
Hydrogens are not under any constraint as such. We have tried to set up the 
simulation following the GROMACS demo as a guideline ( having similar .mdp 

So, a time step of 2fs is OK for me??

Generally speaking, what time step do most people keep?


It depends on the temperature of your system, not the number of steps.
Normally the fastest motions are bond involving hydrogens, and after
that bonds between non-hydrogen atoms.

If you constrain bonds 2fs should be perfectly safe. There's no reason
to go to 1fs (and you gain almost a factor 2 in speed).

A lot of people use 2fs even when they only constrain bonds involving
hydrogens, and that also seems ok. I've done some informal tests, and
when using lincs you can actually often go to 3fs steps, but I cannot
recommend other people to do that - yet.

Neighborsearching should ideally be done at the same _time_ intervals
(not step intervals), so you should decrease nstlist for longer



On Mar 31, 2004, at 6:35 PM, Vivek Raut wrote:

 > Hi,
 > I am running a simulation for 10 ns.
 > How much of a difference does it make to keep the  time step (dt) = 2
 > fs and
 > keeping it = 1 fs??
 > Is there a compromise for accuracy against speed of MD simulations?
 > Will my results vary drastically?>
 > Ideally ( & practically) how much should be the value of dt??
 > ( no. of atoms in my system= 9079)

Graduate Research Assistant,
501 Rhodes Engineering Research Center
Clemson University, Clemson, SC 29634
Tel: 864-650-1431
Email: vraut at clemson.edu


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