Hello,
Thank you Justin and Qinghua!
Can I ask
1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add
a new line of "nstfout=0"?
Yeah, you can add that line, or you can leave it be, the default is set
as ZERO.
2) should I change "nstxout-compressed=5000" to
Thank you Justin and Qinghua!
Can I ask
1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial.
Should I add a new line of "nstfout=0"?
2) should I change "nstxout-compressed=5000" to "nstxout-compressed=5"?
3) Do you mean using "compressed-x-grps=Protein" will set
Hello,
Here is the settings I used in the mdp file, you may consider it.
nstxout = 0 ; save coordinates every 2 ps
nstvout = 0 ; save velocities every 2 ps
nstxtcout = 500 ; xtc compressed trajectory output every
2 ps
nstenergy =
On 12/15/17 7:34 AM, ZHANG Cheng wrote:
Dear Qinghua,
Thank you very much.
Do you mean set "nstvout" and "nstenergy" as 0?
nstenergy is the frequency of writing energy terms to the .edr file. It
has no effect on the .trr, which is only impacted by nstxout
(coordinates), nstvout
Dear Qinghua,
Thank you very much.
Do you mean set "nstvout" and "nstenergy" as 0?
Also, how to set xtc-grps as a group?
The original md.mdp file is:
title = OPLS MD simulation
; Run parameters
integrator = md; leap-frog integrator
nsteps = 1
Hello,
Normally, you don't need to write out the force and velocity, then you
can set nstfout and nstvout as ZERO, then only
the coordinates will be written out in a xtc file.
If you don't care about waters, then you can also set xtc-grps as a
group without waters and counterions.
Best,
Dear Gromacs,
I am following Justin's tutorial of "Lysozyme in Water" to run the MD.
The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less
frequent intervals.
In the md.mdp file, the "dt = 0.002". My understanding is to change the five
"5000" into "5" to achieve
