[gmx-users] About extend the run,,

rama david ramadavidgroup at gmail.com
Sat Jun 2 17:23:40 CEST 2012

Thank you Justin for quick reply ....

On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> To perform these task I am using following command
>> 1. grompp -f <New mdp file just change in  saving output>  -t <.cpt>  -c
>> <.gro
>> file(gro file from position restrained run )>  -o new.tpr
>> 2. tpbconv -s new.tpr -0 extend.tpr  -extend 30000
>> 3. mdrun -v -deffnm extend  -cpi <.cpt> -append
>> Is these approach is correct??
> No.  The new.tpr file contains instructions to run from 20 -> 30 ns.
>  There is no need to then invoke tpbconv.  You would also need a new
> invocation of mdrun, since the output frequencies won't match.  You don't
> want to append those files with mdrun (nor will the checkpoint file likely
> let you)

Extremely Sorry for my carelessness , New mdp files means the same as
previous, with same number of steps, but just change in output frequency

So as per your recommendation and experience  Is any alternative to do
these from 20 ns???

> Second query;
>> To rerun the crash run, users give .cpt file as input to -mdrun,
>> My query is, There are two cpt file a) pre.cpt  b) .cpt ,
>> So which one has to given as input???
> Use gmxcheck to understand the contents of each.  The timestamp will also
> tell you a difference, as will reading mdrun -h for an explanation of what
> the -cpt option is doing

As per the link..
I interpreted following things..

1. I have to use the state.cpt , but in the case  problem to these I have
to use prev.cpt,  I can check there
    content by gmxcheck..

     But my Query is What are may be the potential problems ?? and how to
find them ??

Crash the run is very often with my system, that why I am worried..
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