Jack Shultz wrote:
I'm trying to get the xtc output. The mdp file has these parameters.
Is the nstxtcout what specifiies it to generate xtc?
nsteps = 2000 ; Maximum number of (minimization)
steps to perform
nstenergy = 10 ; Write energies to disk every nstenergy steps
nstxtcout = 10 ; Write coordinates to disk every
nstxtcout steps
Probably. See manual section 7.3.8
Do I need to use this -x flag?
mdrun -nice 0 -s em.tpr -x
No xtc was created though
-x is not a flag - it accepts a filename / filename prefix. Omitting it
entirely will probably generate traj.xtc. Experiment and see.
Mark
On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey <[email protected]> wrote:
On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz <[email protected]>
wrote:
Actually I guess I need to generate the xtc first before I can get the xvg
I am trying to develop a workflow for this
mdrun
g dist calculates the distances between the centers of mass of two groups
g bond calculates distances between atoms
g msd calculates mean square displacements
g rms calculates rmsd’s with a reference structure and rmsd matrices
g rmsf calculates atomic fluctuations
g energy writes energies to xvg files and displays averages
Thats true. First you need to do the simulation 'mdrun' and then analyze the
trajectory (.xtc) and energy (.edr) files generated. It takes quite some
time to figure out the first step 'mdrun' :)
amit
On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey <[email protected]> wrote:
On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz
<[email protected]>
wrote:
Hi I am trying to generate xvg files for my simulation. Which
parameter do I need to specify?
xvg files for what? They are used for data files for 2D plots of
quantities
that can be analyzed...
Can you be more specific?
amit
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Jack
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http://hydrogenathome.org
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