[gmx-users] Continuation of Serial MD simulation in Parallel

[Sridhar Acharya]

Thanks so much for the answer.
I have one more doubt. Could you please answer?
I could make the change and run, but still the following line in the log 
file, "Starting time for run is 0 ps" (BLUE color), appears 
controversial to me.
The log message is as follows.
######################################################
Checking consistency between energy and charge groups...
getting data from old trajectory ...
Reading Coordinates, Velocities and Box size from old trajectory
Will read till time 20000
trn version: GMX_trn_file
Reading frame      60 time 19917.312   Using frame at t = 20000 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x56x75, spacing 0.111 0.114 0.117
splitting topology...
Walking down the molecule graph to make shake-blocks
There are 14390 charge group borders and 12308 shake borders
There are 12308 total borders
Division over nodes in atoms:
 10455 10455 10455 10455
writing run input file...

###############################################################

Dallas B. Warren wrote:

>>So I am generating .tpr file as follows using the command as follows.
>>    
>>
>Does the log message (Highlighted in RED)
>  
>
>>"Velocities generated: ignoring velocities in input trajectory", means
>>    
>>
>that the simulation wont be continuation
>  
>
>>of the earlier one?
>>    
>>
>
>That warning tells you that in your .mdp file you have velocity
>generation on, turn that option off.  You don't want that if you want a
>continuation of the run.  The velocity of the atoms is taken from the
>.trr file that you feed to grompp.
>
>Catch ya,
>
>Dr. Dallas Warren
>Lecturer
>Department of Pharmaceutical Biology and Pharmacology
>Victorian College of Pharmacy, Monash University
>381 Royal Parade, Parkville VIC 3010
>dallas.warren at vcp.monash.edu.au
>+61 3 9903 9524
>---------------------------------
>When the only tool you own is a hammer, every problem begins to resemble
>a nail.
>
>  
>


-- 
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: sridhar at cdfd.org.in
Phone: Lab: 08413-235467*2044
Mobile: 9866147193


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