[gmx-users] mdrun with append option

[Sai Pooja]

On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham <Mark.Abraham at 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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