First, sorry for the revival of this thread so late (maybe it should be better
to start a new one).
> ----- Original Message -----
> From: Dmitri Dubov <[email protected]>
> 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 <[email protected]>
>> > 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
But I have noted just now that using grompp with -t option results in some bug:
after simulation right size of my cubic box (last line of input structure file)
10.00000 10.00000 10.00000
changes in confout.gro to meaningless
0.00000 0.00000 0.00000
To analyse the output properly (e.g. with g_rdf tool) I have to correct this
line manually.
And I'm worried whether this bug effects to my simulation itself, during md
integration of NVE ensemble in vacuum?
--
Rerards,
Dmitri mailto:[email protected]
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