Hi Rana,
And to use ig=-1 for these runnings, in order to get better samplings.
Kind regards,
Pengfei
> On Sep 16, 2017, at 10:22 PM, Elvis Martis <elvis.martis.bcp.edu.in> wrote:
>
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Tue Sep 19 2017 - 19:30:02 PDT
