Error for runnng of plmed driver

[KRISHNA PRASAD GHANTA]

Dear Plumed Developer and users

I am following Combining multiple restraints tutorial for my system of COM restraints , for that I have generated 20 different positions by considering the following .sh file

#!/bin/bash
file="confout.gro"
for i in `seq 0.5 0.1 2.5`;do
mkdir US_$i
cd US_$i

cat >plumed.dat <<EOF
#set up variables for distance calculation
# this is a center of mass of a large group
UNITS LENGTH=nm TIME=ps ENERGY=kj/mol

com1: COM ATOMS=1-22
com2: COM ATOMS=23-44
dist: DISTANCE ATOMS=com1,com2 COMPONENTS

# this makes a new variable, dd, equal to d and periodic, with domain 0,7
# this is the right choise if e.g. the cell is orthorombic and its size in
# z direction is 7 nm.

restraint-dist: RESTRAINT ARG=dist.z KAPPA=1000 AT=$i

PRINT STRIDE=10 ARG=dist.z,restraint-dist.bias FILE=COLVAR$i

EOF

gmx grompp -f final-npt.mdp -c initial.gro -p topol.top -maxwarn 1
cd ..
echo " US_$i completed"
done

for i in `seq 0.5 0.1 2.5`;do
cd US_$i
gmx mdrun -s topol.tpr -plumed plumed.dat -x traj$i.xtc -append -cpi &
until [ -f "$file" ]
do
     sleep 60
done
echo "GRO File found shift to another directory"
cd ..
done

After completing all simulation I did trajcat by considering all 20 trajectory

gmx trjcat -cat -f traj*.xtc -o alltraj.xtc

but when I am trying to do the next step by using .sh file 

#!/bin/bash
for i in `seq 0.5 0.1 2.5`;do

cat >plumed.dat <<EOF
#set up variables for distance calculation
# this is a center of mass of a large group
UNITS LENGTH=nm TIME=ps ENERGY=kj/mol

com1: COM ATOMS=1-22
com2: COM ATOMS=23-44
dist: DISTANCE ATOMS=com1,com2 COMPONENTS

restraint-dist: RESTRAINT ARG=dist.z KAPPA=1000 AT=$i

PRINT STRIDE=10 ARG=dist.z,restraint-dist.bias FILE=COLVAR$i

EOF

plumed driver --mf_xtc alltraj.xtc --trajectory-stride=10 --plumed plumed.dat

done


I got an error 

PLUMED: ################################################################################
PLUMED: 
PLUMED: 
PLUMED: +++ PLUMED error
PLUMED: +++ at Action.cpp:242, function void PLMD::Action::error(const string&) const
PLUMED: +++ message follows +++
PLUMED: ERROR in input to action COM with label com1 : You are trying to compute a CENTER or COM but masses are not known.
PLUMED:         If you are using plumed driver, please use the --mc option
PLUMED: 
PLUMED: ################################################################################
PLUMED: 
PLUMED:                                               Cycles        Total      Average      Minumum      Maximum
PLUMED:                                                    1     0.003708     0.003708     0.003708     0.003708
PLUMED: 1 Prepare dependencies                             1     0.000002     0.000002     0.000002     0.000002
PLUMED: 2 Sharing data                                     1     0.000823     0.000823     0.000823     0.000823
PLUMED: 3 Waiting for data                                 1     0.000002     0.000002     0.000002     0.000002
PLUMED: 4 Calculating (forward loop)                       1     0.001358     0.001358     0.001358     0.001358
terminate called after throwing an instance of 'PLMD::Plumed::Exception'
  what():  
+++ PLUMED error
+++ at Action.cpp:242, function void PLMD::Action::error(const string&) const
+++ message follows +++
ERROR in input to action COM with label com1 : You are trying to compute a CENTER or COM but masses are not known.
        If you are using plumed driver, please use the --mc option
./each-bias-potn-value.sh: line 3: 35180 Aborted                 (core dumped) plumed driver --mf_xtc alltraj.xtc --trajectory-stride=10 --plumed plumed.dat
[iit@localhost final-plumed-file]$ 

#####################################################################################

I can't understand why this error comes for every 20 file. 

It will be helpful for any suggestion .


Thanks

[Giovanni Bussi]

Please read the error:

PLUMED: ERROR in input to action COM with label com1 : You are trying to compute a CENTER or COM but masses are not known.

PLUMED:         If you are using plumed driver, please use the --mc option

It tells everything that you need to fix

Giovanni

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[KRISHNA PRASAD GHANTA]

Dear Giovanni Bussi is there any way to define COM ? because I am using COM as CV. It is not clear to me, If any suggestion is there then please let me know .

****************************************************
Krishna Prasad Ghanta
Research Scholar

Molecular Modeling Laboratory

Indian Institute Of Technology Kharagpur

Kharagpur-721302
Contact no - 8327297650

*************************************

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[Giovanni Bussi]

COM is the acronym for center of mass. Calculating the COM requires knowing the mass of the atoms. The error is telling you that the driver does not know the masses.

Honestly, I cannot imagine how to make the error message clearer, but if you have ideas please let me know.

Giovanni

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[KRISHNA PRASAD GHANTA]

I am newer in plumed so I don't have sufficient knowledge. I can't understand how to solve this problem. I can send you my file If you have some time then please can you check my file ?

[KRISHNA PRASAD GHANTA]

In Belfast tutorial: Umbrella sampling, I have read this tutorial and applied for my system It was Ok. The problem is in this tutorial CV is the phi psi rotation , but for COM as a CV how to proceed that I can't understant, If any other tutorial is there that you know for COM as CV please let me know.

On Saturday, 8 December 2018 16:39:14 UTC+5:30, KRISHNA PRASAD GHANTA wrote:

[Richard André Cunha]

hi, 

you need to provide a file containing the mass and charges of the molecule you are trying to define the center of MASS.
The fastest way to obtain one is to do a 'dry run' using your topology file and a plumed file with "DUMPMASSCHARGE FILE=mcfile". 

if you are using gromacs would be something like this:

gmx mdrun -s topol.tpr -nsteps 1 -plumed plumed.dat

then you can feed mcfile to your driver with the --mc option.

the other way is to use a pdb with mass and charges as the last two columns.

Richard.

[KRISHNA PRASAD GHANTA]

Thanks a lot I will try to apply this. One thing is the here you have specified dry run. Is this the run for test or something other ?

On Saturday, 8 December 2018 16:39:14 UTC+5:30, KRISHNA PRASAD GHANTA wrote:

[Richard André Cunha]

Hi, 

dry run is just a saying since you'll not run a simulation but just one step so you can get it to spit the file with mass and charges. 

Richard.

[KRISHNA PRASAD GHANTA]

Hi 

 Here what will be the mcfile I have tried according to your suggestion 

#set up two variables for com1 and com2 distance

UNITS LENGTH=nm TIME=ps ENERGY=kj/mol

WHOLEMOLECULES STRIDE=1 ENTITY0=1-22 ENTITY1=23-44

DUMPMASSCHARGE FILE=mcfile

com1: COM ATOMS=1-22

com2: COM ATOMS=23-44

dist: DISTANCE ATOMS=com1,com2 COMPONENTS

restraint-dist: RESTRAINT ARG=dist.z KAPPA=1000 AT=2.5

PRINT STRIDE=10 ARG=dist.z,restraint-dist.bias FILE=COLVER2.5

after plumed driver I got the same file as output. I did something wrong ?

On Saturday, 8 December 2018 16:39:14 UTC+5:30, KRISHNA PRASAD GHANTA wrote:

[KRISHNA PRASAD GHANTA]

Another way If I include the pdb file then what will be the format of that pdb file ?

****************************************************
Krishna Prasad Ghanta
Research Scholar

Molecular Modeling Laboratory

Indian Institute Of Technology Kharagpur

Kharagpur-721302
Contact no - 8327297650

*************************************

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[KRISHNA PRASAD GHANTA]

I have followed the dumpmasscharge option in plumed and used the plumed.dat file

c1: COM ATOMS=1-22
c2: COM ATOMS=23-44
PRINT ARG=c1,c2 FILE=COLVER STRIDE=100

DUMPMASSCHARGE FILE=mcfile

then when i am using  gmx mdrun -s topol.tpr -plumed plumed.dat

I got the error as

Program:     gmx mdrun, version 2018.1

Unknown exception:
(exception type: N4PLMD9ExceptionE)

+++ PLUMED error
+++ at Action.cpp:242, function void PLMD::Action::error(const string&) const
+++ message follows +++

ERROR in input to action PRINT with label @2 : cannot find action named c1
(hint! the actions in this ActionSet are: c1 c2 )

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Why this error comes ?

****************************************************
Krishna Prasad Ghanta
Research Scholar

Molecular Modeling Laboratory

Indian Institute Of Technology Kharagpur

Kharagpur-721302
Contact no - 8327297650

*************************************

[Giovanni Bussi]

Hi,

in this case the message is misleading.

To print coordinates of virtual atoms, you should use DUMPATOMS

PRINT only works with values.

I opened an issue so that we remember to fix the error message.

https://github.com/plumed/plumed2/issues/421

Thanks!

Giovanni

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[Aadil Pinjari]

Hello,

I am trying to run metad with  2 CV's, one is distance and other is Coordination number between two sets of atom.

But unfortunately it is showing me the following error. Can you please help me to get out of it.

 Unknown exception:
(exception type: N4PLMD9ExceptionE)

+++ Internal PLUMED error
+++ file Communicator.cpp, line 98
+++ message: you are trying to use an MPI function, but PLUMED has been
compiled without MPI support

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

Thanks,

Aadil