[gmx-users] rerun of trajectory!

[Swetha Vijayakrishan]

dear gromacs users,

i'm trying to simulate a protein solvated in water.I ran the simulation
for 1ns.This was successfully done.Now i want to continue the MD for
another 9ns with the trr file of the 1ns simulation.
So i tried making a continuation input file using tpbconv.i.e

>tpbconv -s b4md_emsd_saksol.tpr -f traj.trr -n md_emsd_saksol.ndx -o
traj_out.tpr

But the command does not seem to work. My .trr file does not seem to be
getting recognized. i'm getting the following error after running the tpbconv
command:

Reading toplogy and shit from b4md_emsd_saksol.tpr
Reading file b4md_emsd_saksol.tpr, VERSION 3.1.4 (single precision)
Reading file b4md_emsd_saksol.tpr, VERSION 3.1.4 (single precision)
Modifying ir->bUncStart to TRUE

READING COORDS, VELS AND BOX FROM TRAJECTORY traj.trr...

Fatal error: File traj.trr not found

Do i have to give any other option in the tpbconv command.
Can anyone please tell me how i can make a continutaion input file for
further rerun of the MD.
Or if i take the output gro file created from the previous 1ns simulation
and use it as input for the grompp command for the 9ns simulation, will it be
equivalent to rerunning from where i left off. Or will the velocities and
energies calculated in the trr file of the 1ns simulation change now as
fresh initail velocities will be assigned for the new run.

will really appreciate if someone can tell me how to go about it and what
exactly can be done to solve the problem.

Thanks & Regards ,

Swetha Vijayakrishnan








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Swetha Vijayakrishnan

Project Assistant
C/O Dr.Shekhar.C.Mande
Centre for DNA Fingerprinting and Diagnostics(CDFD),
ECIL Road,Nacharam,
Hyderabad - 500076

Phone:: Direct: 91-040-7171442
        Indirect: 91-040-7151344/46/47/56 (lab extn 1400)

Fax  :: 91-040-(7155479-7155610>

Email:: swetha at cdfd.org.in
        swethasenorita at yahoo.com