[gmx-users] 4fs timestep in gromacs 4.0

Chris Neale chris.neale at utoronto.ca
Thu Oct 30 17:38:31 CET 2008

Thanks Berk,

My current application is for replica exchange, from which I can not 
extract any dynamic information regardless of heavy hydrogens.

I was under the impression that, when including a protein in the system, 
one would generally desire -vsite to apply to everything except "water 
and in hydroxyl, sulfhydryl or amine groups", which would utilize heavy 
hydrogens. This is based on v4 of the manual, section 6.5, page 125:

"For the hydrogens in water and in hydroxyl, sulfhydryl or amine groups, 
no degrees of freedom can be removed, because rotational freedom should 
be preserved. The only other option available to slow down these 
motions, is to increase the mass of the hydrogen atoms at the expense of 
the mass of the connected heavy atom."

So, would I then use

dt = 0.004
constraints =  all-bonds
constraint_algorithm =  lincs
lincs-iter =  1
lincs-order =  6

after pdb2gmx -vsite -heavyh

or would this make all of my hydrogens heavy, even the ones that are 
already handled by -vsite?


 >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 
 >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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