[gmx-users] time step & constrains

Erik Lindahl lindahl at csb.stanford.edu
Tue Apr 13 22:30:01 CEST 2004

On Apr 13, 2004, at 9:46 PM, Vivek Raut wrote:

>  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??

The gmxdemo mdp files normally constrain all bonds, in which case 2 fs 
is fine. I would hesitate to use 2fs without constraints, but it all 
depends on the system & temperature.

>  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 files).

I think you might be confusing (bond) constraints with position 
(restraints). Both topics are described in the manual.

>  So, a time step of 2fs is OK for me??
>  Generally speaking, what time step do most people keep?

2 fs if you constrain bonds, 1 fs otherwise. This is still pretty 
conservative in many cases, but if you want to take longer steps you 
should probably be prepared to justify why it was ok when trying to get 
a paper published...



More information about the gromacs.org_gmx-users mailing list