[gmx-users] GAP parameter

[Mark Abraham]

Osmair Vital de Oliveira wrote:
> Dear Mark,
> 
> Thank you for the helpful!!. For instance, I have been working with
> molecular dynamics simulation using gromacs for five years...
> Therefore, my ask is an thoughtful question. Contrary with your
> answer..

You didn't technically ask a question :-) In order to maximise your 
chances of getting free help, you don't need to be ingratiating, but you 
should be trying to show respect for your readers' time and expertise by 
expressing yourself clearly. An email like

"Hi, I've been doing molecular dynamics with GROMACS for five years and 
want to simulate system <xxx>. I know I could generate a topology for 
D-glyceraldehyde-3-phosphate for forcefield <yyy> by hand, but was 
wondering whether anybody in the GROMACS community has one already 
they'd be willing to share?"

Now people know exactly what you want and why, and might answer

"Yes, but only for forcefield <zzz>"

"No, and by the way, forcefield <qqq> might be superior for <technical 
reasons>"

"No, but <vvv> published a simulation in journal <www> with a similar 
molecule and you could try contacting them"

"No, but you could check out 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and 
http://wiki.gromacs.org/index.php/Parameterization for some advice on 
generating topologies."

... and they'd be more motivated to give such thoughtful help if they 
get a thoughtful question.

Cheers :-)

Mark

> On Fri, 17 Aug 2007, Mark Abraham wrote:
> 
>> Osmair Vital de Oliveira wrote:
>>> Hi,
>>>
>>> Somebody has force field parameters of the D-glyceraldehyde-3-phosphate
>>> (GAP).
>> If you want to ask a question, please ask an thoughtful question. You
>> should probably also check out
>> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and
>> http://wiki.gromacs.org/index.php/Parameterization
>>
>> Mark