Re: [gmx-users] checkpointing in 4.0.7

issue now (due to time lack), but use tpbconv for continuation runs. I though that someone perhaps knows already solution. Best regards, Leonid Mark Abraham wrote: > On 25/03/2010 10:01 PM, Dr. Leonid Yelash wrote: > >> Hello everybody, >> >> does anyone have a simila

[gmx-users] checkpointing in 4.0.7

Hello everybody, does anyone have a similar problem writing checkpoints from Gromacs 4.0.7? I have two Gromacs versions, 4.0.5 and 4.0.7, compiled for bluegene. The 4.0.5 writes state.cpt during mdrun and at the end of simulation too. The 4.0.7 does it at the end of the run only, but not during t

Re: [gmx-users] msd

Hello together, i refer here to the problem with msd mentioned at the beginning of September (see also below): i calculate msd this time for monomers (not for molecules as before) and i still observe finite size effects for chains if they include fixed bonds ([constrains]), however this effect

[gmx-users] -append on jugene overwrites trr

Hello all together, in my compilation of Gromacs 4.0.5 on JUGENE (a Blue Gene/P machine in Jülich), the -append option does not work properly. When i restart a simulation from a checkpoint, the mdrun recognizes the checkpoint and -append (one can see it in md.log), but instead of appending to md.l