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

[Mark Abraham]

----- Original Message -----
From: Dmitri Dubov <ddubov at ngs.ru>
Date: Thursday, May 27, 2010 19:11
Subject: Re[2]: [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>

> > I expect that either 

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

> No, this way is unsuccessful, maybe due to somewhat contradictive instructions:
> grompp supplies newtpr with usual options
> tinit                    = 0
> nsteps                   = 100000
> simulation_part          = 1

> and from old_state.cpt the system finds itself on 100000th step already and stops.

OK. Presumably some more cunning choice of .mdp options would work, or using grompp, tbconv -extend and then mdrun.

> > 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 :-)

> And the latter variant is working! More precisely I use
> grompp -f new -t old_state.cpt -c oldtpr -o newtpr 
> mdrun_d -s newtpr


Mark