Dear Acoot
this is a question for gromacs, NOT amber...
On 4/10/12 9:25 AM, Acoot Brett wrote:
> Dear All,
>
> There are 2 mini.mdp (for energy minimization) for gromacs.
>
>
> The first mini.mdp is as following:
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0 ; Stop minimization when the maximum force< 1000.0 kJ/mol/nm
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0 ; Short-range electrostatic cut-off
> rvdw = 1.0 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
> The second mini.mdp is as folowing:
> ; ions.mdp - used as input into grompp to generate ions.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0 ; Stop minimization when the maximum force< 1000.0 kJ/mol/nm
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME ; Treatment of long range electrostatic interactions
> rcoulomb = 1.4 ; Short-range electrostatic cut-off
> rvdw = 1.4 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions
> The difference is the cut-off. One is 1.4,the other is 1.0. Can anyone explain their difference on the influence of the MD result?
> Suppose I use AMBER 99SB force field, will you lease tell me how can decide the value of the above cut-offs?
> Cheers,
> Acoot
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Apr 10 2012 - 06:30:05 PDT
