[gmx-users] Gromacs and restraints

Matteus Lindgren matteus.lindgren at chem.umu.se
Wed Jul 16 16:15:54 CEST 2008

Hi all

I´m new to gromacs, having previously worked with Charmm. 

After looking through articles and gromacs tutorials it seems many use the
SETTLE algorithm for water, restraining both water angle and bonds, as well
as restraining all bonds in proteins, while using a timestep of 2fs. I
believe in Charmm it is common practice to only use SHAKE on X-H bonds, not
angles or X-X bonds, for the same timestep. I got curious, why the different
setups for the different programs, force fields? 


I will be running protein in explicit water simulations and need a timestep
of 2fs. Forces and energies in the system will be analyzed. What restraint
setup should I choose?





Matteus Lindgren 

Graduate student 


Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Tel: +46 (0)90 786 53 68
e-mail:  <mailto:barbara.addario at chem.umu.se> matteus.lindgren at chem.umu.se


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