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

2011-03-10 Thread Justin A. Lemkul
Henri Mone wrote: Hi Mark, Thanks for your feedback. The simulations are running now again. I got one questions, I think it will be also of interest for the others on the mailinglist. I used "grompp" with the "-t state0.cpt" option, are the starting velocities taken from the cpt files or are

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

2011-03-10 Thread Henri Mone
Hi Mark, Thanks for your feedback. The simulations are running now again. I got one questions, I think it will be also of interest for the others on the mailinglist. I used "grompp" with the "-t state0.cpt" option, are the starting velocities taken from the cpt files or are the assigned randomly

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

2011-03-08 Thread Mark Abraham
On 8/03/2011 9:41 PM, Henri Mone wrote: 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,

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

2011-03-08 Thread Henri Mone
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

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

2011-03-07 Thread Mark Abraham
On 7/03/2011 8:23 PM, Henri Mone wrote: 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.

[gmx-users] RMSD truncation Restart simulation problems

2011-03-07 Thread Henri Mone
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