# Re: [AMBER] AMBER 99SB force field used by GROMACS

From: Acoot Brett <acootbrett.yahoo.com>
Date: Tue, 10 Apr 2012 22:03:22 -0700 (PDT)

Dear Lorenzo,
If I run different cutoff MD, will you please suggest how to judge whether a cutoff value is suitable or not?

Cheers,

Acoot

________________________________
From: Lorenzo Gontrani <l.gontrani.caspur.it>
To: Acoot Brett <acootbrett.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, 11 April 2012 12:39 AM
Subject: Re: [AMBER] AMBER 99SB force field used by GROMACS

Dear Acoot, the value of vdw cutoff generally used with amber inputs
is 8 Ang (that is 0.8 nm, if you use Gromacs conventions).
Dispersion interactions are very "steep", i. e. they decay very
quickly, since they depend on the inverse sixth power of the distance
(R^-6).
The use of large cutoffs gives, therefore, very little improvement on
the energy, and causes a HUGE increase of calculation times (as the
"pairlist" of vdw interactions gets very big). My advice is to test
different cutoff values for very short trajectories, and see what is
the smallest value that you can use.

Good luck

Lorenzo

2012/4/10 Acoot Brett <acootbrett.yahoo.com>:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

--
==========================================
Lorenzo Gontrani
Research associate of CNR-ISTM (Rome Tor Vergata)
EDXD group of University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
=========================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 10 2012 - 22:30:02 PDT
Custom Search