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

Mark Abraham mark.abraham at anu.edu.au
Thu May 27 07:57:19 CEST 2010

----- Original Message -----
From: Dmitri Dubov <ddubov at ngs.ru>
Date: Thursday, May 27, 2010 15:41
Subject: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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! 

Sure, discontinuity is guaranteed from the loss of precision.

> 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?

Probably not.

>How can I get the full precision in output structure file RIGTH after mdrun? Or it is mandatory to use trjconv with -ndec option?

I expect that either 

grompp -f new -o newtpr
mdrun -s newtpr -cpi old_state.cpt


grompp -f new -t old_state.cpt -o newtpr
mdrun -s newtpr

will do what you want. Please report back if one or both work :-)

Or, maybe you can use old-style .trr and .edr output as input to grompp, so long as you planned that in advance. A checkpoint-file approach is superior, however.

> What is the default precision of .trr trajectory file in single and double precision modes?

Machine precision.


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