[gmx-users] 4fs timestep in gromacs 4.0

Berk Hess gmx3 at hotmail.com
Thu Oct 30 12:34:21 CET 2008


Just use:
pdb2gmx -vsite h
and use LINCS with all bonds constrained
I would use lincs_order=6 with dt=4 fs, see the P-LINCS paper for details:

I would not use heavy hydrogen, since that affects the dynamics.
I always use 4 fs time steps for my ion-water systems and see no differences
with 2 fs simulations in extremely accurate rdf's.

I would use lincs_order=6

> Date: Wed, 29 Oct 2008 22:32:25 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] 4fs timestep in gromacs 4.0
> Hello,
> I am interested in trying the 4 fs timestep options for an  
> opls-protein/tip4p-water system. I will of course do some quick NVE  
> tests to ensure that the energy does not drift massively, and also do  
> some other tests that look at some properties that should equilibrate  
> rather quickly. Also, I realize that there is no substitute for  
> reading the literature.
> Still, I am hoping to get some indication of how this was intended to  
> be utilized in gmx4. Can I just run pdb2gmx -vsite -heavyh and apply  
> LINCS to all-bonds? The information in the gmx4 manual is nicely  
> detailed about how each type of hydrogen should be treated, but I am  
> not clear how to achieve this in my .top.
> Searches for vsite and heavyh reading only the 2008 posts did not give  
> me much indication about this.
> Thanks,
> Chris.
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