You can check the manual for what does it mean.
> On Sep 19, 2017, at 9:25 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> 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
>>>> _______________________________________________
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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
