Dear all,
I have read few papers regarding the photo dissociation event such
as Myoglobin heme-ligand bond deletion to induce the photodissociation in
MD simulation.
Could you please tell me the procedure how can i perform the
photodissociation mechanism in Gormacs and which force field have to
Justin,
In accordance to the manual I've re-launched my simulation by the command
mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append
where md_initial is the name of the files from the run which I want to continue.
As the result this produce new files with the default
On 9/15/12 10:03 AM, James Starlight wrote:
Justin,
In accordance to the manual I've re-launched my simulation by the command
mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append
where md_initial is the name of the files from the run which I want to continue.
As the
Jusin,
yes, the initial files were named as the md_initial
the simulation was resumed correctly but all output data was saved
into new set of files with the default names. In my case I want that
the resummed simulation data will write to the existing (md_initial)
files without creation of new
On 9/15/12 10:11 AM, James Starlight wrote:
Jusin,
yes, the initial files were named as the md_initial
the simulation was resumed correctly but all output data was saved
into new set of files with the default names. In my case I want that
the resummed simulation data will write to the
In that case I've obtain error
Fatal error:
Failed to lock: md_init.log. Already running simulation?
What does it means ? the md_init.log is present in the wor dir
2012/9/15 Justin Lemkul jalem...@vt.edu:
On 9/15/12 10:11 AM, James Starlight wrote:
Jusin,
yes, the initial files were
On 9/15/12 10:17 AM, James Starlight wrote:
In that case I've obtain error
Fatal error:
Failed to lock: md_init.log. Already running simulation?
What does it means ? the md_init.log is present in the wor dir
That means mdrun expects your files to be named md_init not md_initial as
you
On 16/09/2012 12:17 AM, James Starlight wrote:
In that case I've obtain error
Fatal error:
Failed to lock: md_init.log. Already running simulation?
What does it means ? the md_init.log is present in the wor dir
Appending to an old run requires that all the filenames are identical
between
On 9/15/12 10:33 AM, James Starlight wrote:
There is no errors in the filenames
In the above example init and initial names were used for simplicity :)
What you accomplished was confusion. Always use real file names. If you know
enough to filter information and create a false reality,
On 9/13/12 1:12 AM, James Starlight wrote:
Dear Gromacs Users!
I'm looking for possible way to resume trajectory calculations after
that calculations have been stoped.
Typically in such cases I start new task using cpt file from
incomplete run. This produce new trajectory which start from
Justin,
I've used
grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o
incomplete.tpr
mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append
where incomplete.cpt was checkpoint from previous run and -o
incomplete.tpr was the name for new trajectory (in that case its equal
On 9/13/12 9:56 AM, James Starlight wrote:
Justin,
I've used
grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o
incomplete.tpr
mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append
where incomplete.cpt was checkpoint from previous run and -o
incomplete.tpr was the
Dear Gromacs Users!
I'm looking for possible way to resume trajectory calculations after
that calculations have been stoped.
Typically in such cases I start new task using cpt file from
incomplete run. This produce new trajectory which start from the last
frame of previous run. After that I
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