Re: Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC?

Hi, In fact I simulated 30 nanoseconds, but I found the system reached equilibrium at 4.4 ns (by analyzing RMSD, Energy and visualizing, etc.) and did not change significantly in the last 25 ns. Thus I want to do an essential dynamics for the first 5 ns. I also calculated the covariance matrix for

Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC?

s that the movement of protein IN THIS 0.6ns is believable?     -Original Message-From:"David van der Spoel" <[EMAIL PROTECTED]>Sent:2006-09-11 09:20:33To:"M. Yan" <[EMAIL PROTECTED]>Title :Re: [gmx-users] May I use "-b" and "- e" in the c

[gmx-users] May I use "-b" and "- e" in the cosine co n tent calculation of PC?

ndicator than the RMSD from thestarting structure. Note that the number of possible conformationsincreases rapidly with increasing RMSD, and you'll find the RMSD leveloff well before you have true convergence. For larger systems this maytake 15-25 ns or more! Hope it helps, Tsjerk On 9/11/06

[gmx-users] calculate the interaction energy between different parts of protein

Hi dear friends, I want to analyze the interaction energy between two parts of protein, for instance, residue 57-62 and residue 104-109. g_energy does not work because the file ener.edr did not record this items. How to calculate it from the trajectory file?   Thanks.   3G 时 代 来 临 了，坚 决 对 传 统 邮 箱

Re: [gmx-users] calculate the interaction energy between differentparts of protein

Thank you, Mark I modify the .mdp file as follows: energygrps = Protein sol Cl  --> energygrps = res57_62 res102_109   and make tpr file: grompp -f md.mdp -c pr_out.gro -p topol.top -o rerun.tpr -n index.ndx mdrun -rerun test.xtc -s rerun.tpr It gives warings: WARNING: Some frames do not contain v

Re: Re: [gmx-users] calculate the interac tion energy between different parts of pr otein

Thank you, Mark I modify the .mdp file as follows: energygrps = Protein sol Cl  --> energygrps = res57_62 res102_109   and make tpr file: grompp -f md.mdp -c pr_out.gro -p topol.top -o rerun.tpr -n index.ndx mdrun -rerun test.xtc -s rerun.tpr It gives warings: WARNING: Some frames do not contain ve