[gmx-users] Recover velocity from trr file and coordinates from xtc file

[Alan Dodd]

You need full precision coordinates (i.e. trr and not xtc) for an accurate restart.  You might be able to bodge it with the use of trjconv/trjcat or something to make a "pretend" trr with coordinates and velocities, but I wouldn't count on it.
Oh, and a restart file is a tpr, not a gro.  Making a .gro file is easy - see manual page on trjconv.  The manual is useful.


----- Original Message ----
From: Myunggi Yi <myunggi at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, November 30, 2007 3:54:17 PM
Subject: Re: [gmx-users] Recover velocity from trr file and coordinates from xtc file

Thank you for your help.
However, I can't understand how to generate gro file from trr and xtc files.
I'm sorry. I'm a beginner.

Would you let me know exact command? or where can I find?

Again, I saved velocity only in trr file, and I have xtc file (only coordinates).
I have edr file also.

I found the following to make the restart file (gro file).

tpbconv -s eq5.tpr -f eq5.trr -e eq5.edr -o eq6.tpr -time 6870.000

Since I have velocity only in the trr file, I can't apply this.

Any idea?




On Nov 29, 2007 11:17 AM, Alan Dodd < anoddlad at yahoo.com> wrote:
> http://wiki.gromacs.org/index.php/Doing_Restarts
> 
> You can make a gro with what you have.  You *may* be able to continue your run properly.  Read the above link. 
> 
> 
> ----- Original Message ----
> From: Myunggi Yi <myunggi at gmail.com>
> To: gmx-users at gromacs.org 
> Sent: Thursday, November 29, 2007 4:06:06 PM
> Subject: [gmx-users] Recover velocity from trr file and coordinates from xtc file
> 
> Dear Gmx users,
> 
> Can I make a gro file (restart file) from trr (I saved only velocities) 
> and xtc file (which has the coordinates)?
> If I can, how can I do this job?
> I'm a beginner.
> 
> Have a nice day.
> 
> 
> 
> --
> Best wishes,
> 
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
> 
> Office: (850) 645-1334 
> http://www.scs.fsu.edu/~myunggi
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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi



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