[gmx-users] Help with Error Message

Justin Lemkul jalemkul at vt.edu
Sun Aug 25 03:37:10 CEST 2013

On 8/24/13 9:26 PM, The One And Only wrote:
> that's something i know nothing about; I just graduated from high school
> and I have no background or experience in open source projects or programs
> like pymol/gromacs. My professor wants me to be able to produce a setup,
> simulation, and analysis within a week so I'm pretty desperate right now in
> terms of getting help. Do you know how to get the right .pdb file in my
> working directory?

Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. 
  Google can find lots of good ones.  Producing a quality simulation cannot be 
rushed, and if you don't know the fundamentals of navigating the command line 
and directory structure, it's nearly impossible.  You need to invest time in 
learning the environment before doing anything, I'm afraid.  Just to give a bit 
of perspective, we used to train our undergrads for nearly a full semester (at 
least 2-3 months) before requiring them to do any "real" work.  At least a week 
or two of that time was spent getting used to command line and Linux in general.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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