[gmx-users] Restart dmpc membrane

[Carl-Johan Högberg]

So how do i do if i would like to change for example how often the 
trajectory is dumped for the continuation run?

Carl-Johan


David van der Spoel wrote:

>On Tue, 2004-06-01 at 16:11, Carl-Johan Högberg wrote:
>  
>
>>Thats true but in  tpbconv i use the .tpr file i used when i originally 
>>started the simulation. When i created this .tpr with grompp i used an 
>>.mdp file. Or should i use grompp to create a new .tpr file before i use 
>>tpbconv?
>>    
>>
>No.
>
>the first time you run grompp, grompp generates the velocities. mdrun
>just reads them from the tpr. with tpbconv you will get the last
>velocities from your trajectory.
>  
>
>>Carl-Johan
>>
>>
>>David van der Spoel wrote:
>>
>>    
>>
>>>On Tue, 2004-06-01 at 14:11, Carl-Johan Högberg wrote:
>>> 
>>>
>>>      
>>>
>>>>Ok it seems to work! Thanks.
>>>>
>>>>Another question. In my .mdp file i have the option:
>>>>
>>>>gen_vel = yes
>>>>
>>>>When i restart my simulation with tpbconv do i get new velocities or 
>>>>does the simulation continue with the velocities in the .gro or .trr file?
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>If you use tpbconv you don't use an mdp file.
>>>
>>>
>>> 
>>>
>>>      
>>>
>>>>Best regards
>>>>Carl-Johan
>>>>
>>>>
>>>>
>>>>David van der Spoel wrote:
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>>>On Tue, 2004-06-01 at 12:38, Carl-Johan Högberg wrote:
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>>>Hi gmx-users
>>>>>>
>>>>>>I have some problems restarting a dmpc membrane simulation. The 
>>>>>>simulation has been running for 30ns and now a want to start it again. 
>>>>>>When using tpbconv i get the following error:
>>>>>>
>>>>>>WARNING: The simulation uses pressure and/or temperature coupling,
>>>>>>       the continuation will only be exact when an energy file is supplied
>>>>>>
>>>>>>And also:
>>>>>>
>>>>>>0 steps (0 ps) remaining from first run.
>>>>>>You've simulated long enough. Not writing tpr file
>>>>>>
>>>>>>Anybody who has any suggestions how to solve this problem?
>>>>>>  
>>>>>>
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>>tpbconv -f -s -e -o -extend 1000
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>>>Best regards
>>>>>>Carl-Johan
>>>>>>  
>>>>>>
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>


-- 
Carl-Johan Högberg
Department of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm
Sweden
Phone: +46-8-162373