Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

2007/4/5, David van der Spoel <[EMAIL PROTECTED]>: Ryogo Sugitani wrote: > David, > > How about adding [ nonbond_params ] in your ff???nb.itp file > as shown in p.88 of the user's manual? > I believe it will override the default vdw interaction for that > particula

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

David, How about adding [ nonbond_params ] in your ff???nb.itp file as shown in p.88 of the user's manual? I believe it will override the default vdw interaction for that particular atom-type pair. (Assuming you want to use combination rule #1 just for that atom-type pair) If I miss your point,

Re: [gmx-users] How to implement dihedral restraints

Thanks for your reply, >>Chris The test I ran was just rotating a side chain of an amino acid residue over one of its dihedral angle 360 degrees with dihre_fc = 8000. I originally thought fc = 8000kJ/mol unit^2 would give fluctuation of about the half the unit size since I use fc = 8000kJ/mol nm

Re: [gmx-users] How to implement dihedral restraints

Hello, I have a quick question on dihedral restraints. What is the unit of dihre_fc in .mdp file? (It's not on the User's manual) > Add this to your .mdp > ;dihedral restraints > dihre = simple > dihre_fc= 100 ; or whatever value you desire > dihre_tau =

Re: [gmx-users] Coulomb 1-4 interactions

Justin, What is your fudgeQQ value in ffamberXX.itp? This value (I think the default is 0.8333) should be the reciprocal of scaling factor used in Amber's input file (I think the default is 1.200). Check amber's manual specific parameter name for it. (I don't remember off my head right now.) Be

Re: [gmx-users] ZN HIS binding

Hi, I think you have to make this line HIS NE2 1 ZIH ZN 1 0.25HISZZIH as HIS NE2 1 ZIH ZN 3 0.25HISZZIH because zinc needs to make 3 special bonds. Also check NE2-Zn distances are all within 10% of 0.25 (Assuming you've alr