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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
========================================
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