Re: [gmx-users] Constraints and efficency

2011-01-05 Thread David van der Spoel
On 2011-01-05 21.44, Elton Carvalho wrote: On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham wrote: On 5/01/2011 5:53 AM, Elton Carvalho wrote: [...] Does the larger timestep allowed by eliminating high-frequency O-H vibrations outweigh the time needed by SETTLE? Most definitely. Typical GROMACS

Re: [gmx-users] Constraints and efficency

2011-01-05 Thread Elton Carvalho
On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham wrote: > On 5/01/2011 5:53 AM, Elton Carvalho wrote: >> [...] Does the larger timestep allowed by eliminating >> high-frequency O-H vibrations outweigh the time needed by SETTLE? > > Most definitely. Typical GROMACS simulations report up to a few percen

Re: [gmx-users] Constraints and efficency

2011-01-04 Thread Mark Abraham
On 5/01/2011 5:53 AM, Elton Carvalho wrote: Hello, fellow GROMACS users! I noticed many users applying constraints to their simulations, be it SETTLE to water molecules or LINCS to some other species. This brings about an efficiency concern once that after each Verlet step some systems of couple

[gmx-users] Constraints and efficency

2011-01-04 Thread Elton Carvalho
Hello, fellow GROMACS users! I noticed many users applying constraints to their simulations, be it SETTLE to water molecules or LINCS to some other species. This brings about an efficiency concern once that after each Verlet step some systems of coupled equations must be solved in order to apply t