[gmx-users] CCl4 solvent

[xieyh at hkusua.hku.hk]

Dear GMX users:

I'd like to simulate protein in CCl4 solvent.
But before using that model provided in GMX attatchment, I have some questions
to get help from you.
 
1. What is the use of ccl4_box.mdp? Because in the spc model, I just find
spc.itp and spc216.gro. I am confused about how and when to use this
ccl4_box.mdp file.

2. The given ccl4 box is under opls FF. If I want to use it in ffgmx FF, whether
I should change sigma and epsilon to C6 and C12 as the follows:
Assuming my comb_rule under ffgmx is set to 1, then
C6(i)=4*epsilon(i)*sigma(i)^6,   C12(i)=4*epsilon(i)*sigma(i)^12.
Is that correct¡HPls give me a confirmation.

And, how about the modification to other files, such as ffgmx.atp ffgmx.rtp
etc.
 
3. What is the definition of bonds, angle etc items in the CCL4.itp? I could not
find them.

The first time to use other solvent, so I am sincerely waiting for your reply.

 

Thanks and regards
Xie YH