Re: [gmx-users] B-factor to large? Input for TLS

Hi Mark, Thanks for your reply. I will check if the reference structure and the trajectory fit. Cheers Henrey On Mon, Nov 7, 2011 at 9:15 PM, Mark Abraham wrote: > On 5/11/2011 11:05 AM, Henri Mone wrote: >> >> Dear Gromacs Users and Experts, >> >> I want to calcu

[gmx-users] B-factor to large? Input for TLS

Dear Gromacs Users and Experts, I want to calculate from my xtc trajectory the B-factor and the anisotropic temperature factor. I'm using following gromacs command: $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb I want to input the resulting PDB file to the "TLS" S

[gmx-users] trjorder, what and how does es count (amount solvent atoms or molecules)?

Dear Gromacs Users, I'm using "trjorder" with the following options: $ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r 0.35 -nshell system0.35.nshell.xvg As the first group I select all the atoms of a single TYR residue, which is part of a larger protein. As the second group

Re: [gmx-users] RMSD truncation Restart simulation problems

he assigned randomly from a Boltzman distribution. Meaning are the new simulations starting fresh or are they acontinuation from the previous ones? Thanks, Henri On Tue, Mar 8, 2011 at 1:54 PM, Mark Abraham wrote: > On 8/03/2011 9:41 PM, Henri Mone wrote: >Ah yes, I remember now. mdrun tr

Re: [gmx-users] RMSD truncation Restart simulation problems

Hi All, hi Mark, Here are some more details. The outputs and error messages are attached at the end of the e-mail. After truncation I get the error message [1a], gromacs has problems with the checksum of the trr fles. After truncation the trajectories (xtc, trr) have the same length of 27752 frames

[gmx-users] RMSD truncation Restart simulation problems

Dear Gromacs Users/ Experts and Beginners, I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations stooped abruptly and therefore the replicas have uneven information. One of the checkpoint differ in time and frame compared to other replicas. My case is very similar to the problem re

[gmx-users] Extending REMD simulation

Dear Gromacs experts, I started a REMD simulation which terminated succesfully after 4830ps. I now want to extend it to 50ns. I'm using Gromacs 4.0.3 which supports checkpoint files. I got now around 40 files with the ending "*.cpt" and "*_prev.cpt". I couldn't find any documentation on how to ex

[gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation

Calculate observed "Acceptance Ratio" from REMD simulation Dear Gromacs users, I used the Gromacs how-to [1] to setup a REMD simulation. The targeted acceptance ratio was P_acp=15%, I used the temperature generator web-service [2] to get the temperature spacing. From the test simulation I want to

[gmx-users] g_rotacf create tpr from pdb

Der Gromacs users and dear Justin, The gromacs tutorial does not really tell how to create a "tpr" without a "mdp" file. The standard procedure in the tutorials is to use the program "grompp" which always requires a "mdp" file. But for calculating the autocorrelation function I only need the coord

[gmx-users] g_rotacf create tpr from pdb

Dear Gromacs experts and newbies, The program "g_rotacf" (calculates the autocorrelation function) requires as input for the -s option either a "tpr", "tpb" or "tpa" file. I does not accept for the -s option a PDB file :- ( . How can I create from a "pdb" file a "tpr" file? The program "pdb2gmx" c