[gmx-users] Non-conservation of total energy while using structure file to resume the simulation

Dmitri Dubov ddubov at ngs.ru
Thu May 27 07:05:54 CEST 2010

Dear GMX'ers!

I simulate system of about hundreds of water molecules in NVE ensemble with md integrator. Every 100 ps I need to change slightly some parameters, say, electric field and to continue the simulation from this point. As I realize I cannot go on my run using the checkpointing and tpbconv in this case. Therefore I try to use the output structure file confout.gro which contains both coordinates and velocities at the end of the previous step. 

The problem is in the total energy. Within every 100-ps run the energy drift is quite low. But when I start the next step, at its very beginning I see the considerable jump in the total energy and the temperature comparing with the end values of previuos step. 
NOTE that it is the case even when I change NOTHING in my job.mdp file! 

To my knowledge the coordinates and velocities define exactly the energy and the temperature. Now I suspect the only reason - low precision of confout.gro. So, my questions are:
Is there another reason for the total energy non-conservation in my simulation?
How can I get the full precision in output structure file RIGTH after mdrun? Or it is mandatory to use trjconv with -ndec option?
What is the default precision of .trr trajectory file in single and double precision modes?

Hoping for your help,
 Dmitri                          mailto:ddubov at ngs.ru
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