[gmx-users] mdrun with append option

[Sai Pooja]

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.

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> 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>> wrote:
>>
>>
>>
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