[gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 15 17:02:20 CEST 2007

Nicolas Schmidt wrote:
> (a) Nope, my .mdp-file don't reads that. So I think I don't use one.
> (b) I use some different software, that does exactly what I want. It's 
> very reliable and it's telling me that the pressure of a 2CLJ-fluid with 
> all the set parameters should be different. Since I wanna do the exact 
> same thing, the higher pressure kind of points out that in fact I'm not 
> doing the same.
> (c) Exactly! Bondtype 5 doesen't imply a length parameter. So therefor 
> I'm using a constraint. David told me to do so. I'm really unsure at 
> this point, this is why I posted my issue.

Huh? Bond type 5 is only used for manipulating exclusion generation. You 
seem to want a constrained bond, so you should either use one from 5.4 
in your topology, or use the constraint algorithms on all bonds. Please 
describe clearly both what you are doing, and what you are trying to do, 
because at the moment I don't understand either of them!

> Still: Though I thought I don't have to specify the 
> electrostatics-section since my molecule doesn't have any charges (or 
> does it???), what to do to totally switch the electrostatics off?

You should be reading section 7.3 of the manual closely and making these 
choices actively, with reference to earlier in the manual where needed. 
You'll need to understand well how both this other software and GROMACS 
are doing the calculation in order to duplicate the ensemble averages.


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