[gmx-users] (no subject)

[K.A. Feenstra]

> Justin Lorieau wrote:
> 
> Hi,
> 
>     I'm interested in looking at backbone N-H or Ca-H order > parameters, and comparing then to and NMR experiment. I have a
> couple of questions..
> 
> (1) My simulations were done with the GROMACS force field that
> does not include the hydrogens explicitly. Although these
> hydrogens exist in the trajectory files, can I accurately get
> good rotational autocorralation data from these?

If they exist in the trajectory, they exist *explicitly* in the forcefield as well. So, in that case, yes, the rot-acf will be 
accurate. But, in the Gromacs (ffgmx) and Gromos (ffG43*) 
forcefields, only the backbone N-H hydrogen is present, not the 
Ca-H.

You can use the 'protonate' program (included with Gromacs) to
add all hydrogens explicitly to your trajectory...

> (2) I'm using the g_rotacf program to do my analysis, looking
> at individual N-H bonds at specific residues (using the '-d'
> parameter). Is there an easier way to extract a list of
> rotational autocorrelation times for a type of bond (ex: backbone N-H
> bonds) or backbone model-free order parameters?

g_rotacf

> I appreciate any advice and suggestions, thanks.

You're welcome...


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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