On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 3/02/2011 6:15 AM, Sai Pooja wrote: > >> The problem is solved with grompp i.e. I use the -t .cpt option. However, >> now appending does not work. I remember Mark said in a previous mail that a >> certain environment variable can allow appending to happen even in such >> cases. I would liek to try that out. >> >> No, I said that an environment variable can override the mechanism that > blocks ensemble changes in mdrun. > So how can I use this environment variable.. I might be asking an absurd question since I don't really understand what an environment variable is. But I would definitely liek to experiment with it, since I am in the process of trying out these different options and figuring out which would be the best. I also need to understand something. What exactly does the tpbconv do when only -s and -nsteps or -extend options are supplied - it seems that it takes all the information(mass, topology, restraints) from the previous tpr file and just changes the init_step parameter and the number of steps till which the simulation should run. Now if that is the case, I am still unable to understand that if the cpt file is NOT provided to mdrun (or a mismatched one is provided), how does mdrun obtain the coordinates, velocities, box-dimensions of the last frame. If it doesn't use the ones of the last frame, what does it really use? If it gets them from the new_tpr file, and the new_tpr file gets it from previous_tpr file via tpbconv, then how does that ensure continuation from the last frame, because the previous_tpr file might have been compiled even before the simulation started. And as far as I know, it is purely an input file to mdrun and has no information on the last coordinates/velocities of the mdrun. You may have answered this before but I have tried and failed in understanding. I would request you to help me in understanding the above. I would really appreciate it. Regards Pooja
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