[gmx-users] Restarting a gromacs calcluation

[Triguero, Luciano O]

>> Dear Users,
>>
>> Thank for your help. I started a 10 ns simulation, but it dies because of
>> an error in the cluster PBS system, so I want to continue the simulation
>> from the last (r,v) point. May I still use tpbconv to restart from that
>> last point and continue the simulation.
>>    
Check where your trr or edr file ends using gmxcheck -f or -e. The
shorter will be used by tpbconv for your new tpr. Specify tpbconv with
-f and -e.
 
Dear,
 
Thank for your answer. I still have a problem. Do you mean (-f and -e) or (-f or -e)
 
I checked my trr and edr files and edr files ends first, then I typed:
 
tpbconv   -s md_input.tpr -f <>.trr -e <>.edr -o md_cont.tpr
 
and got the following error message:
 
++++++++++++++++++++++++++++++++++++++++++++++++++
Opened md_minim_energy.edr as single precision energy file
Reading frame   4000 time 4000.000           
Last frame read 4876                               
WARNING: Incomplete frame: nr   4877 time 4876.000     
-------------------------------------------------------
Program tpbconv, VERSION 3.3.1
Source code file: enxio.c, line: 401
Fatal error:
Could not find frame with time 4884.000000 in 'md_minim_energy.edr'
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
However, tpbconv runs without error when I provide only option -e <>.edr. Is it correct to restart 
a calculation with the .tpr file generated with only -e <>.edr option. Will be then possible to concatenate trajectories correctely?
 
Advices,
 
Thank for your time,
 
Luciano 
 
 

>
> Sure - as far as I know. It will generate new .tpr, which you will use for
> starting the simulation - when it is finished, simply concatenate
> trajectories, energy files with trjcat and eneconv.
>
> Milan
>
>  
>> Thank again,
>>
>> Luciano
>>
>> Dr. Luciano Triguero College of Art and Science Department of Physics and
>> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118
>> Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
>>
>> ________________________________
>>
>> From: gmx-users-bounces at gromacs.org on behalf of Yang Ye
>> Sent: Fri 3/16/2007 8:49 AM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Restarting a gromacs calcluation
>>
>>
>>
>> Can you be more specific? Continue or start new simulation. Use tpbconv
>> to extend your simulation.
>>
>> On 3/16/2007 9:37 AM, Triguero, Luciano O wrote:
>>    
>>> Dear users,
>>>
>>> How do I restart a gromacs simulation?
>>>
>>> Ciao,
>>>
>>> Luciano
>>>
>>> Dr. Luciano Triguero College of Art and Science Department of Physics and
>>> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box
>>> 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office:
>>> 305-284-3938 _______________________________________________
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