[gmx-users] mdrun with append option

[Justin A. Lemkul]

Sai Pooja wrote:
> When I use .cpt file with tpbconv, I get the error pasted below. I 
> checked the cpt file with gmxdump and it is not empty and has the same 
> number of atoms.
> 

So use grompp, as I suggested before.  Using gmxdump to verify the number of 
atoms is also not what I suggested; it can be used as a means to verify that the 
proper coordinates and velocities were assembled in the new .tpr file.

-Justin

> Reading toplogy and stuff from rex_1.tpr
> Reading file rex_1.tpr, VERSION 4.5.1 (single 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
> Modifying ir->bContinuation to TRUE
> READING COORDS, VELS AND BOX FROM TRAJECTORY restart1.cpt...
> 
> -------------------------------------------------------
> Program tpbconv, VERSION 4.5.1
> Source code file: tpbconv.c, line: 451
> Fatal error:
> Number of atoms in Topology (8962) is not the same as in Trajectory (0)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 
> On Tue, Feb 1, 2011 at 1:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Sai Pooja wrote:
> 
>         I am doing a manual replica exchange(generalized hamiltonian
>         rem) after every mdrun. If the replica exchange is successful,
>         then I "exchange checkpoint files". For example, consider the
>         following:
>          Simulation parameters:....................B1.........B2
>         Replicas(coordinates and velocities):.R1.........R2
>          0. Tpbconv to extend simulation time ( using -s, -o and -nsteps
>         ONLY)
>         1. Mdrun run - 500 steps = 1ps
>         2. Attempt exchange - NOT SUCCESSFUL
>         3. Exchange implementation: SKIP 4.Continue to next step
>          .....
>         0. Tpbconv to extend simulation time ( using -s, -o and -nsteps
>         ONLY)
>         1. Mdrun run - 500 steps = 1ps
>         2. Attempt exchange - If successful, exchange
>         3. Exchange Implemented by - exchanging checkpointing files
>         4. Continue to next step
>          0. Tpbconv to extend simulation time ( using -s, -o and -nsteps
>         ONLY)
>         1. Mdrun with exchanged .cpt files -NOW this is where the
>         problem shows..
>              i) The log, xtc files are not appended when beginning after
>         a step with a successful exchange attempt:/According to Mark's
>         previous mail, this could be a result of mismatch in ensembles.
>         Which means that the .cpt is ignored - implying that the mdrun
>         in B1 DOES NOT start from R2./
>          
> 
> 
>     Sounds like a reasonable conclusion.
> 
> 
>         Therefore, to make R1 run in B2 and R2 run in B1, do I need to
>         supply .cpt to tpbconv instead of mdrun after a successful
>         exchange step?
>          
> 
> 
>     Either tpbconv or grompp can do this.  Check the resulting .tpr with
>     gmxdump to make sure it's using the proper coordinates, velocities,
>     etc from the .cpt file and you'll have your answer as to whether or
>     not it's working as you want.
> 
>     -Justin
> 
>         To summarize:
>         APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM
>         INTERESTED IN IS A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS
>         POINTED OUT ABOVE.
>          I hope my dilemma is clear now.
>          Pooja
>                          
>         On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================