[gmx-users] [EXT] Re: 500ns simulation

[Smith, Iris]

Hi Raag,

Within your .mdp file there is a "Run parameters" section that has the following line items (see below). If you want to achieve 500 ns you need to increase the nsteps and multiply it times the timestep - ensuring that the timestep is appropriate enough for what you want to achieve. See below example with a 2 fs timestep.

; Run parameters
nsteps		= 250000000	; 0.002(dt) * 250000000(nsteps) = 500000 ps (500 ns)
dt	 	= 0.002		; 2 fs
 
Best,

Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | (216) 445-7885
 
 

On 7/4/18, 2:43 AM, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Soham Sarkar" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of soham9038 at gmail.com> wrote:

    Increase the number of steps
    
    On Wed, 4 Jul 2018, 12:07 pm Quyen V. Vu, <vuqv.phys at gmail.com> wrote:
    
    > Take simulation time= timestep (dt) * number of steps (nstep)
    >
    > On Wed, Jul 4, 2018, 12:48 Soham Sarkar <soham9038 at gmail.com> wrote:
    >
    > > Change in the number of time steps
    > >
    > > On Wed, 4 Jul 2018, 10:54 am Raag Saluja, <saluja.raag at gmail.com> wrote:
    > >
    > > > Hi!
    > > >
    > > > What changes do I make to the mdp files provided by you in the lysozyme
    > > > tutorial, to make it a 500ns simulation?
    > > >
    > > > Thanks in advance!
    > > >
    > > > Regards,
    > > > Raag
    > > > --
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