----- Original Message ----- From: Dmitri Dubov <[email protected]> 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 <[email protected]>
> 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 or 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. Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
