[gmx-users] restarting a run using tpbconv

[N-J.M. Macaluso]

I have 2690 frames in my .trr file. Will providing the energy file in 
tpbconv solve the problem?

On Jul 21 2007, Yang Ye wrote:

>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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