Re: [gmx-users] Problems with Jacobi diagonalization

Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12

Re: [gmx-users] Problems with Jacobi diagonalization

Hi there Tsjerk- There are a lot of helpful people on this list! I transferred my gromacs files to a different TeraGrid computer that runs gromacs-4.0.2, and now g_covar and the other diagonalizing routines work! I don't know what was wrong with gromacs-3.3.3 on that first computer, since I tried

Re: [gmx-users] Problems with Jacobi diagonalization

Hi Dayle, Quite a number of posts here :) Okay, so there may indeed (still) be a mismatch. Maybe good noting that g_covar will also accept a .pdb file as reference. One way to be sure that things go right is to convert the .tpr to .pdb using the index with the group 'TDR': editconf -f topol.tpr

Re: [gmx-users] Problems with Jacobi diagonalization

Thanks, Mark- I re-ran a short MD simulation with TDR as the only xtc group, and used tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar with an index.ndx that contains only TPR (just to be safe!), g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx and I still get the Jacob

Re: [gmx-users] Problems with Jacobi diagonalization

Or rather than modifying the .top use tpbconv with an index file to generate a new .tpr Tom --On Wednesday, April 01, 2009 21:15:34 -0400 "Justin A. Lemkul" wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.x

Re: [gmx-users] Problems with Jacobi diagonalization

Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and

Re: [gmx-users] Problems with Jacobi diagonalization

Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that t

Re: [gmx-users] Problems with Jacobi diagonalization

Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't ge

Re: [gmx-users] Problems with Jacobi diagonalization

Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined "xtc_grps = TDR" in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't un

Re: [gmx-users] Problems with Jacobi diagonalization

Hi Tsjerk, Thank you for your quick and helpful response. I defined "xtc_grps = TDR" in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what "shuffling" o

Re: [gmx-users] Problems with Jacobi diagonalization

Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to con