[gmx-users] a residue move in extremely large scale in MD

Justin Lemkul jalemkul at vt.edu
Sat Aug 11 02:21:40 CEST 2012

On 8/10/12 8:19 PM, Acoot Brett wrote:
> Dear Justin,
> Can you explain to me what do you mean for "trjconv -pbc mol -ur compact followed by trjconv -center". Does it mean 2 steps command, with the first step as "trjconv -pbc mol -ur compact" and the second step as "trjconv -center"? Or can we merge it as a single step step?

Those are two separate invocations of trjconv.

> Second, will you please tell me in " If the outcome of the analysis before and after PBC correction are the same", which analysis can be used as the "outcome" for the analysis?

Whatever analysis you choose to do will result in some outcome.  If the results 
are different before and after PBC correction, then PBC effects are important 
and are contributing to some erroneous observation.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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