[gmx-users] Problem with the MDS extended trajectory in GROMACS 5.0.4

PAULAMI CHATTERJEE chatterjee_paulami at yahoo.co.in
Thu Jul 9 21:26:51 CEST 2015

Thank you very much for your response. So you are suggesting that  
'gmx mdrun -s final_monomer.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append'
instead of
'gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append' (which I have used for the extended simulation)

can solve my problem. I will surely try this one.

Thanks and RegardsPaulami 

     On Thursday, 9 July 2015 6:54 PM, soumadwip ghosh <soumadwipghosh at gmail.com> wrote:

    Say your initial mdrun command for 30 ns were as follow

grompp_mpi -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o md_0_1.tpr
mdrun_mpi -deffnm md_0_1

Then you should get the files such as md_0_1.xtc, md_0_1.log,
md_0_1.edr, md_0_1.cpt, md_0_1.trr and so on

Then you obtain a new tpr file say new_100ns.tpr using tpbconv or gmx
convert with appropriate flags.
Now, if you want to extend your simulation by a certain amount of time
and want all your previous files appended the exact command should be
something like

mdrun_mpi -s new_100ns.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append

I did it once and coordinates were saved from 0ns all the way to 100ns
and the same md_0_1.xtc, md_0_1.edr etc files were apeended without
any difficulty. I am not quite sure but there's no harm in trying.

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