[gmx-users] File editing - only one layer of water around a molecule

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 13 18:13:40 CEST 2012

Lara Bunte wrote:
> Hi
> You are totally right. I am sorry. It is just so frustrating if you read 
> the complete help more than once, understand nothing and than here all 
> the time, that I should read the help. :-(
> I like Gromacs and I am happy that it is free and I am very thankful for 
> all the help here in the mailing list.
> But I also have to say (please don't take this an attack): If you are a 
> total beginner and have no good knowledge about basic chemistry, it is 
> really tough and frustrating reading the manual and help. There should 
> be more help, especially how to type it in. Not everywhere but in the 
> i.e. in the beginning of the manual a few words about that. 
> I am from engineering and now I am in the physical chemistry. I want to 
> learn! I am reading in the manual, the tutorials and in Chemistry for 
> beginner books, but all the stuff is pretty hard if you are new in the 
> topic....

If you're new to chemistry, and especially computational chemistry, then you're 
not only trying to learn chemistry, but Linux/Unix and specialized software that 
makes use of it.  That is usually too much at once and leads to frustration. 
You have to learn to walk before you can run.  When we train new members of our 
lab, it's a stepwise process and they usually spend a few weeks or months 
learning basic (and unfortunately, sometimes repetitive and boring) things 
before we even let them touch anything useful or truly productive ;)  Certain 
prerequisites are assumed, and by necessity, have to be, otherwise the Gromacs 
manual becomes bloated by recapitulating information that is already well 
covered in other places.

> About the topic:
> Is there no way only to use the .pdb file? How do I create from a .pdb a 
> rtp file. With pdb2gmx and than grompp?

Please note that I said .tpr file, not .rtp.  They are wildly different.  The 
.tpr file is used to run a simulation, which I suspect we all assumed was 
something you had done and thus had accessible to you.  A coordinate file and 
corresponding topology, coupled with an .mdp file, are needed to assemble the 
.tpr file using grompp.



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


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