[gmx-users] A question about general MD procedure

jackyxh at 163.com jackyxh at 163.com
Wed May 3 11:35:51 CEST 2006

Hi,dear GMX group and other users:

First of all, I wanna thank Yang Ye, David, Mark and others for your instant replies to most our online questions.

I am a new user of gromacs(version 3.3). I want to do carbon nanotube MD (to obtain the relationship between axial compressive force and the tube's corresponding deformation).

I have done the demo, read the manual and hundreds of online "Mailing lists" and I have even run EM on my own carbon nanotube model with Yang Ye's help (though a little problem seems still exist with that model). 

But finally I am completely confused on what I should do next step. Should I run PR and then MD as the demo shows? Then how could I add the axial compression on the model? I know GMX can make that, but it seems that I need a guide to show me the proper entrance of a big building before I can begin to find the certain room.

Any suggestion on the following principled helps will be greatly appreciated:
1,Should I run EM, PR and then MD as a procedure like demo shows in my model?
2,How could I add the axial compression on the model (either axail forces or axail deformation)? in which step (PR or MD)? and with which file (.mdp? .top?)? 
Thanks for all your attentions!
With respect,
Jacky Allon
jackyxh at 163.com
If you send me one, I will always Re you three, friendship, help or anything else except emails and money:) ――Jacky Allon
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