Re: [gmx-users] Re:confusion regarding tpbconv

[Xavier Periole]

On Tue, 13 May 2008 13:21:12 +0530
 "sudheer babu" <[EMAIL PROTECTED]> wrote:

shall we mention in this way?
steps:
1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr
2- mdrun -v -deffnm new.tpr

check (gmxcheck -h) the content of trr and edr files!
.trr should contain coordinates and velocities
.edr should contain energies

at the same time, 7 ns you mention I think.

Thanks in advance.


On Mon, 12 May 2008 15:10:32 +0530
"Anamika Awasthi" <[EMAIL PROTECTED]> wrote:

Dear Friends,
       If my simulation crashed because of power failure, then as I know
there are two option to restart the Job.
        One is GROMPP and another is 'tpbconv', in 'grompp' we have to do
some changes in md.mdp, but 'tpbconv' takes everything automatically,
tpbconv needs only .trr and .edr and it takes previous simulation's frame

as

initial frame for restart and generate new .tpr file.
     This .tpr we should use for md rerun.

your concept is correct but you should just run the new tpr file, not rerun
it
with mdrun.
steps:
1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr
2- mdrun -s new.tpr

        I just want to ask, whether my this concept is correct or not. If

I

am not correct please help me to correct this.

Thanks in advance
     Anamika

-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole <http://md.chem.rug.nl/%7Eperiole>
-----------------------------------------------------

-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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