ERROR in input to action DUMPMASSCHARGE with label @7 : charges were not passed to plumed.

[Fene Gao]

Dear plumed users and developers,

I am running Metadynamics using plumed 2.5 with cp2k 7.1 and am getting the following error: ERROR in input to action DUMPMASSCHARGE with label @7 : charges were not passed to plumed.

My plumed.dat file is as follows:

UNITS LENGTH=A TIME=fs

# this is a center of mass of a guest molecule

com1: COM ATOMS=218-223

# this is a center of ring

c0: CENTER ATOMS=83,88,106

d: DISTANCE ATOMS=com1,c0 COMPONENTS

PRINT STRIDE=1 ARG=* FILE=COLVAR

DUMPATOMS ATOMS=com1,c0 FILE=coms.xyz STRIDE=1

DUMPMASSCHARGE FILE=mcfile

Any help would be much appreciated.

Thanks,
Fen'e Gao

[Gareth Tribello]

This is pretty self explanatory.  The MD code is not passing charges to PLUMED so you can’t output them with the DUMPMASSCHARGE.  This makes sense as you are using a quantum code so there is some debate about how to extract the charge from the electron density.  If you delete the line  line DUMPMASSCHARGE from your input it should work.

Gareth

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[Fene Gao]

Hi Gareth,

When I delete the line DUMPMASSCHARGE from my input it does work.

This problem arises from my post-processing of WHAM Umbrella Sampling refer to the PLUMED tutorial(https://www.plumed.org/doc-v2.5/user-doc/html/belfast-4.html).

When I execute command: mpiexec -np 11 plumed driver --ixyz all.xyz --plumed plumed-wham.dat --multi 11,  I got an error: 

+++ 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

[liujy08:41967] *** Process received signal ***

[liujy08:41967] Signal: Aborted (6)

[liujy08:41967] Signal code:  (-6)

[liujy08:41967] [ 0] /lib64/libpthread.so.0(+0xf5d0)[0x2b8b1fdde5d0]

[liujy08:41967] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b8b20021207]

[liujy08:41967] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b8b200228f8]

[liujy08:41967] [ 3] /lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2b8b1f6107d5]

[liujy08:41967] [ 4] /lib64/libstdc++.so.6(+0x5e746)[0x2b8b1f60e746]

[liujy08:41967] [ 5] --------------------------------------------------------------------------

mpiexec noticed that process rank 4 with PID 0 on node liujy08 exited on signal 6 (Aborted).

--------------------------------------------------------------------------

It tells me that I need to provide a file containing the mass and charges of the molecule I am trying to define the center of MASS. So, I added the line DUMPMASSCHARGE in my plumed input file.

I don't know if there is any other way to solve it besides this one or how can I obtain a file containing the mass and charges of the molecule, If any suggestion is there then please let me know.

Best regards,

Fen'e Gao

[Gareth Tribello]

You only need the masses first of all.  You don’t need charges.  You know what atoms are in the molecules you are simulating and you know how to use the periodic table of the elements so you can make the file yourself.  It should look like this:

#! FIELDS index mass charge

0 1 0

1 2 0

2 3 0

3 4 0

The masses are in the second column.

Gareth

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[Giovanni Bussi]

I was answering the same. On the other hand, probably we should add an option to DUMPMASSCHARGE such as IGNORE_CHARGES that does the same (writing zero charges)

Giovanni

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[Giovanni Bussi]

Mm, there is already!

DUMPMASSCHARGE ONLY_MASSES

However, you should then add a new column with zero charges for this to be correctly read by driver.

So perhaps the correct thing is to make it so that if driver does not find the charge column it sets them to zero?

Giovanni

[快乐女孩]

Hi Giovanni,

Thank you very much for your guidance. 

After trying, I found that Plumed could not automatically set the charges to zero if driver does not find the charge column, so we need to manually add a column with zero charges to the file abtained from DUMPMASSCHARGE ONLY_MASSES.

Kind regards,

Fen'e Gao

------------------ 原始邮件 ------------------

发件人: "plumed-users" <giovann...@gmail.com>;

发送时间: 2021年3月31日(星期三) 晚上9:37

收件人: "plumed-users"<plumed...@googlegroups.com>;

主题: Re: [plumed-users] ERROR in input to action DUMPMASSCHARGE with label @7 : charges were not passed to plumed.

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