[gmx-users] Setting total simulation time

[Justin Lemkul]

On 6/3/13 12:42 PM, Parker de Waal wrote:
> Thanks Mark,
>
> Using the above I ran gmxcheck -f nvt.trr
>
> Here is the resulting out put
>
> Last frame        500 time 1000.000
>
> Item        #frames Timestep (ps)
> Step           501    2
> Time           501    2
> Lambda         501    2
> Coords         501    2
> Velocities     501    2
> Forces           0
> Box            501    2
>
> Does this mean I can interpret this as 1 ns of simulation with output every
> 2 ps?
>

Yes.

> Also I thought when I assigned values for output at 1000, such as nstxout =
> 1000, that I would get an write of data every 1 ps?
>

All of the nst* options (as the name implies and the manual explains) are given 
in number of steps, not time units.  Thus the nst* options are dependent upon 
the value of dt to be given meaning in terms of time.  With dt = 0.002, and 
nst(whatever) = 1000, you get output every 2 ps.

-Justin

> I'm moderately confused!
>
> Parker
>
>
> On Mon, Jun 3, 2013 at 11:02 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Try smaller numbers and periods for a test run, and see the machinery work.
>> gmxcheck on the output files is your friend!
>>
>> Mark
>>
>>
>> On Mon, Jun 3, 2013 at 4:40 PM, Parker de Waal <Parker.deWaal09 at kzoo.edu
>>> wrote:
>>
>>> Hi GMX-users,
>>>
>>> If I wanted to run a 1 ns simulation take snapshots every 1 ps would
>> these
>>> be the correct input parameters?
>>>
>>> Thanks!
>>>
>>> ; Run parameters
>>> integrator      = md
>>> nsteps          = 500000
>>> dt              = 0.002
>>> ; Output control
>>> nstxout         = 1000
>>> nstvout         = 1000
>>> nstenergy       = 1000
>>> nstlog          = 1000
>>> --
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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