Hi,
Breaking down your simulations only means running ten simulations of 10ns each restarting from the previous run.
Use nstlim = 5000000 and dt = 0.002.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Rana Rehan Khalid <rrkhalid.umich.edu>
Sent: 17 September 2017 00:37
To: AMBER Mailing List
Subject: Re: [AMBER] simulation time
Can you please guide me how i can break simulation for ten runs as you
mention or send me url link.
Thank you so much sir for your help.
On Sat, Sep 16, 2017 at 2:34 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hi,
> 100 ns is common these days.
> But what I recommend here is, run your MD in parts instead of one single
> run.
> Here you can break 100 ns into 10 runs of 10 ns each or 20 runs of 5 ns
> each.
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> Sent: 17 September 2017 00:01
> To: AMBER Mailing List
> Subject: Re: [AMBER] simulation time
>
> Thanks Elvis. Is this normal practice in MD to run the simulation for
> 50000000 steps?
>
> Regards
>
> On Sat, Sep 16, 2017 at 2:14 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > HI
> > all the time scales in the input file are mentioned in ps.
> > For instance dt = 0.002 means 2fs time step.
> > if you want to know the time simulation, then time (ps) = nstlim * dt.
> > for 100 ns = 100000 ps with dt = 0.002 ps your nstlim must be 50000000.
> >
> > Best Regards
> > Elvis Martis
> > Mumbai, INDIA.
> >
> > ________________________________________
> > From: Rana Rehan Khalid <rrkhalid.umich.edu>
> > Sent: 16 September 2017 22:22
> > To: AMBER Mailing List
> > Subject: [AMBER] simulation time
> >
> > Hi Everybody
> >
> > If I want to run the simulation in amber for 100ns what would be the
> values
> > of these flags. Actually i am confused between pico and nano.
> >
> > nstlim=50000,
> > dt=0.002, this is for 100ps duration time.
> >
> > nstlim=?? for 50 nenosec
> >
> > Regards
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
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> >
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Received on Sat Sep 16 2017 - 20:30:02 PDT
