[gmx-users] Position Restraints with NVT and NPT

[zanemarkson]

Dear All GMX Users

I have some questions about doing NPT equilibration while keeping my protein
(or small molecule) fixed. I know there have been a lot of discussion about
this topic but after reading them I am still confused. So could anyone
please give me some clear answer or insight about the following questions?
Thank you in advance!!! 

1) By including the pores.itp into my topology file, am I really position
restraining the chosen atoms? I did a NVT equilibration with a pores.itp
included in my topology file and "define = -DPOSRES" written in my .mdp
file. After the mdrun was done, I used g_traj to check the coordinates of
those "fixed" atoms. However, instead of seeing non-changed coordinates, I
can see the Cartesian coordinates of those "fixed" atoms changed. The
magnitude of changing is in the order of 0.001nm. 

2) So if including pores.itp is not a good option for fixing chosen atoms,
what is the best way to do it. What will the .mdp file look like? What I am
really trying to do here is simply just to equilibrate my solvent molecule
while  keeping my protein (or small molecule ) fixed. 


Again, thank you in advance!


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