Hirdesh: Yes my apologies... I actually meant to give the link I used at the end but it slipped my mind. It was the page I used heavily when I was new with ptraj. I use it as my "cheat-sheet" because a) it uses 95% of what I need in ptraj and b) it's the first thing to show up in a "ptraj tutorial" search via google. Very convenient.
http://ambermd.org/tutorials/basic/tutorial5/
Tangent to Ross: looking forward to your GTC talk.
Trevor
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Tuesday, September 21, 2010 10:46 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] molecular dynamics simulation-water-box-diffution problem
Hi Hirdesh,
> I request to elaborate it a little bit more. It is ok for persons having
> great hand with amber but for for beginners, it may be not so clear that
how
> to use these three lines.. what will be the input and what will be the
> output. Please suggest the tutorial if you can.
You cannot expect a tutorial for everything. The tutorials are designed to
get you started but beyond that one is expected to actually seek to
understand what is going on. They are encouraged to make you think
independently and troubleshoot things for yourself. Such independent
troubleshooting is a vital skill that you will need to master if you want to
become a successful research scientist.
I suggest looking at the AMBER Tools manual, specifically read the ptraj
section. Each of the commands Trevor mentioned is clearly and concisely
explained there along with syntax.
If you have not already done so I would also suggest starting with Tutorial
B1 here: http://ambermd.org/tutorials/ and then work progressively through
each one in turn.
Good luck,
Ross
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Received on Wed Sep 22 2010 - 01:00:03 PDT
