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 <[email protected]>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 <[email protected]
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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