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? Regards /Matteus Matteus Lindgren Graduate student Department of Chemistry Umeå University SE-901 87 Umeå, Sweden Tel: +46 (0)90 786 53 68 e-mail: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
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