[gmx-users] Regarding continuation of mdrun

[alkasrivastava at iitb.ac.in]

Hello everyone

I have a doubt regarding the extension of simulation in newer version of
gromacs (4.0.4).

1)
If simulation has completed and one wants to extend it further the option
used is

tpbconv -s full_part3.tpr -extend timetoextendby -o full_part4.tpr

and then mdrun as usual with an additional flag for cpt file like this

nohup mpirun -np 4 mdrun_mpi_d -v -s full_part4.tpr -c full_part4.gro -o
full_part4.trr -x full_part4.xtc -e full_part4.edr -g full_part4.log -cpi
state.cpt >& full_part4.job &

After this what i am getting is that it is changing the files names as :
full_part4.trr to full_part4.part0002.trr

Is is normal?


2) My another doubt is that whether I have to give cpt file in tpbconv as
well?


If I am doing that

tpbconv -s full_part3.tpr -extend 10000 -o full_part4.tpr -f state.cpt

I am getting a note like this

.................................................................................
Reading toplogy and shit from full_part3.tpr
Reading file full_part3.tpr, VERSION 4.0.4 (double precision)

NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv.
      Continuation should be done by loading a checkpoint file with mdrun
-cpi
      This guarantees that all state variables are transferred.
      tpbconv is now only useful for increasing nsteps,
      but even that can often be avoided by using mdrun -maxh


READING COORDS, VELS AND BOX FROM TRAJECTORY state.cpt...

Skipped cpt frame      0: step      0 time    0.000
cpt frame 0 (step 0, time 0) is incomplete

Using frame of step 0 time 100000
Extending remaining runtime of by 10000 ps (now 67500000 steps)
Writing statusfile with starting step          0 and length   67500000
steps...
                                 time      0.000 and length 135000.000 ps

......................................................................................




But I am not getting any notes when i am using tpbconv without any cpt file


i.e. tpbconv -s full_part3.tpr -extend 10000 -o full_part4.tpr

Reading toplogy and shit from full_part3.tpr
Reading file full_part3.tpr, VERSION 4.0.4 (double precision)
Extending remaining runtime of by 10000 ps (now 67500000 steps)
Writing statusfile with starting step          0 and length   67500000
steps...
                                 time      0.000 and length 135000.000 ps



3)If the simulation has been crashed then there is no need to make the tpr
file only the mdrun with cpt file and append option is all that required
like this

nohup mpirun -np 4 mdrun_mpi_d -v -s full_part3.tpr -c full_part3.gro -o
full_part3.trr -x full_part3.xtc -e full_part3.edr -g full_part3.log -cpi
state.cpt >& full_part3.job &

Is it correct?

Could anyone please clear my doubts.

Thanks in advance
Alka