Colvar and hills file not created

[Stanley kapoor]

Hi,

I am running following command:

mpirun -np 4 mdrun_mpi -v -deffnm topol -multi 4 -replex 5000 -plumed plumed.dat

My plumed.dat file is included in plumed.dat.0, plumed.dat.1, plumed.dat.2, plumed.dat.3 files. All these files also contain following line:

PRINT ARG=t1,t2,t3,t4 STRIDE=2000 FILE=COLVAR

The above command runs successfully with no error but at the end no such COLVAR and HILL file was created.

Please help me out.

[Stanley kapoor]

This is my first run using plumed2. Has anybody encountered such a problem before?

Any kind of suggestions are welcomed.

[Giovanni Bussi]

Hi can you check from the md0.log if plumed is actually invoked? Giovanni

Inviato da iPhone

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[Stanley kapoor]

On Saturday, February 22, 2014 11:12:52 AM UTC+5:30, Stanley kapoor wrote:

Hi,

Hi Giovanni,

Yes I can see from my *.log file that plumed is actually invoked as evident from following lines (copied from my log file):

 

PLUMED: PLUMED is starting

PLUMED: PLUMED compiled on Feb 19 2014 at 15:49:11

PLUMED: Please cite this paper when using PLUMED [1]

PLUMED: For further information see the PLUMED web page at http://www.plumed-code.org

PLUMED: Molecular dynamics engine: gromacs

PLUMED: Precision of reals: 8

PLUMED: Running over 1 node

PLUMED: Number of atoms: 33

PLUMED: GROMACS-like replica exchange is on

PLUMED: File suffix: .0

PLUMED: FILE: plumed-common.dat

PLUMED: Action TORSION

PLUMED:   with label t1

PLUMED:   between atoms 1 5 11 13

PLUMED:   using periodic boundary conditions

PLUMED: Action TORSION

PLUMED:   with label t2

PLUMED:   between atoms 11 13 15 21

PLUMED:   using periodic boundary conditions

PLUMED: Action TORSION

PLUMED:   with label t3

PLUMED:   between atoms 13 15 21 23

PLUMED:   using periodic boundary conditions

PLUMED: Action TORSION

PLUMED:   with label t4

PLUMED:   between atoms 21 23 25 31

PLUMED:   using periodic boundary conditions

PLUMED: END FILE: plumed-common.dat

PLUMED: Timestep: 0.001000

PLUMED: Relevant bibliography:

PLUMED:   [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)

PLUMED: Please read and cite where appropriate!

PLUMED: Finished setup

 

I am not able to figure out the reason for the file being not created.

[gareth....@gmail.com]

The log file suggests that the print command is not being read. Can you send your plumed.dat files. 

Sent from my iPad

[Stanley kapoor]

Hi Gareth Tribello,

I have attached two of my files. Please have a look at them. I am failed to understand why the print command is not being read. Do I need specify it explicitly in plumed-common.dat as well?

Thanks in advance.

On Saturday, February 22, 2014 11:12:52 AM UTC+5:30, Stanley kapoor wrote:

[Giovanni Bussi]

Hi,

it seems that your files contain dos newlines. Can you try to process them first with dos2unix?

Giovanni

[Stanley kapoor]

Hi,
I have converted previous files to unix using:

sed 's/^M$//'
and checked for successful conversion using:
if awk  '/\r$/{exit 0;} 1{exit 1;}' myFile
then
  echo "is DOS"
fi

Still my COLVAR file was not created. But when I give PRINT FILE=COLVAR line in plumed-common.dat file instead of in plumed.dat.* , 4 COLVAR files named COLVAR.0, COLVAR.1, COLVAR.2, COLVAR.3 (all same) were created. 
I think somehow we have to include plumed.dat.0 etc files in plumed-common.dat file as well. This is because even if I don't create plumed.dat.0 etc files, the command runs successfully (but with no COLVAR file creation) with just one plumed-common.dat file.
In short, I believe that it is reading only plumed-common.dat file and not other files.Please help me out.

On Saturday, February 22, 2014 11:12:52 AM UTC+5:30, Stanley kapoor wrote:

[Stanley kapoor]

I think this is the problem of syntax in plumed2 while carrying out bias exchange metadynamics.

Has anyone (who has done BEMD using plumed2 before) encountered such a problem? Any suggestions are highly welcomed.

On Saturday, February 22, 2014 11:12:52 AM UTC+5:30, Stanley kapoor wrote:

[Stanley kapoor]

I have got stuck here. Please help me resolve the problem.

Eagerly waiting for reply.

On Saturday, February 22, 2014 11:12:52 AM UTC+5:30, Stanley kapoor wrote:

[Carlo Camilloni]

Hi I tried your input locally and it works correctly.

Can you try to run it adding at the end of the plumed-common.dat file this:

FLUSH STRIDE=10

Carlo

[Stanley kapoor]

Thank you Carlo for your reply. May be I am missing something, but still I am unable to create COLVAR file even after adding FLUSH STRIDE=10
I still believe it is not reading plumed.dat.# files and reading only one file i.e. plumed-commaon.dat file (since the command runs perfectly even without having plumed.dat.# files in the pwd). Is there a way to check that?

Please help me resolve the problem.

On Saturday, February 22, 2014 11:12:52 AM UTC+5:30, Stanley kapoor wrote:

[Carlo Camilloni]

Hi, if it is reading only the plumed-common file this means that:

You are using

-plumed plumed-common.dat

Or

You have a file called plumed.dat that is been read instead of the plumed.dat.#

Or you have a keyword endplumed at the end of the plumed-common.dat file, otherwise I cannot see any reason why it shouldn't work

Carlo

Sent from my iPhone

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[Stanley kapoor]

Thank you so much Carlo for pointing out my mistake.  Uptil now I was using :
-plumed plumed-common.dat

But now the issue is resolved. Thanks once again.

On Saturday, February 22, 2014 11:12:52 AM UTC+5:30, Stanley kapoor wrote: