[gmx-users] restarting a run using tpbconv

[Yang Ye]

The velocity is in the trr file. How many frames you have in 
protein.trr? What's its last frame?
You also need to supply the energy file to tpbconv.

On 7/21/2007 10:15 PM, N-J.M. Macaluso wrote:
> This may be a trivial question, but how do you save velocities in this 
> case? Would it be in the .mdp file or in the tpbconv command?
>
> Thanks for your help,
>
> Max
>
> On Jul 21 2007, David van der Spoel wrote:
>
>> N-J.M. Macaluso wrote:
>>> Hello,
>>>
>>>    I am running a very long simulation, and the cluster I'm using 
>>> has a wall time. I am using tpbconv to restart my simulations from a 
>>> frame in the last run, but this doesn't seem to be working. When I 
>>> analyze the second trajectory, the starting structure looks 
>>> identical to the starting structure I had from the beginning. I am 
>>> not sure if I am correctly using tpbconv.
>>>
>>> I'm taking the completed trajectory of the run I want to continue 
>>> and start the second run from the 1300 ps frame:
>>>
>>> tpbconv -s protein.tpr -f protein.trr -o protein2.tpr -time -1300
>>>
>>> Then I submit the continued job with this command:
>>>
>>> mdrun -s protein2.tpr -o protein2.trr -c protein2.gro -g 
>>> protein2.log -e protein2.edr -np 16
>>>
>>> Like I said, it doesn't seem to start the second run from the 
>>> specified frame, but rather runs the simulation from the starting 
>>> structure. I would appreciate any help.
>>
>> you should save your velocities at regular intervals.  it will start 
>> from that last save velocities (t=0 in your case).
>>>
>>> Thanks,
>>>
>>> Max Macaluso
>>>
>>>
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>>
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