[gmx-users] Group-specific differences in RMS fluctuation results via g_rmsf

I would like to calculate the RMS fluctuations of residues in an active site, using the following command and options: g_rmsf -f x16traj.trj -s x16topol.tpr -n index2.ndx -b 1000 -res -o rmsf.xvg -od rmsdev.xvg When the program asks me to "Select group(s) for root mean square calculation",

Re: [gmx-users] opls parameters

Hi Mark, On Dec 3, 2006, at 7:20 AM, Mark Abraham wrote: So evidently opls_005 is a nitrogen atom... so what's with the "C2 6"? Further, there is no bonded interaction in ffoplsaa.rtp for "C2", but there is C_2... So I really don't understand what is going on. The "6" doesn't belong to

Re: [gmx-users] opls parameters

Dear Mark, I think C2 is CH2 group, rather than N atom because of its mass (refer to opls_071, opls_072), and it is said in ffoplsaa.atp that types 1-134 are from the united-atom OPLS. Dongsheng On Sun, 2006-12-03 at 17:20 +1100, Mark Abraham wrote: > > Sorry i'm probably being a bit slow, but