Question about simplemd

[Lei Wu]

Dear All,

 

I am using Plumed 2.1.2 and trying the tutorial 

 http://plumed.github.io/doc-v2.1/user-doc/html/belfast-10.html

When I used the given files, in and input.xyz  to run simplemd with the command,

      plumed simplemd < in

, I encountered an error. The plumed complained that the file  plumed.dat cannot be found.  It makes me 

confused, because the document doesn't mention how to provide simplemd with plumed.dat file.

Thank you for your kind help.

Lei

The message:

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

Starting configuration           : input.xyz

Final configuration              : output.xyz

Number of atoms                  : 108

Temperature                      : 1.200000

Time step                        : 0.005000

Friction                         : 1.000000

Cutoff for forces                : 2.500000

Cutoff for neighbour list        : 3.000000

Number of steps                  : 50000

Stride for trajectory            : 100

Trajectory file                  : trajectory.xyz

Stride for statistics            : 10

Statistics file                  : energies.dat

Max average number of neighbours : 10000

Dimensionality                   : 3

Seed                             : 0

Are atoms wrapped on output?     : F

PLUMED: PLUMED is starting

PLUMED: Version: 2.1.2 (git: Unknown) compiled on Jun 27 2015 at 14:22:18

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: simpleMD

PLUMED: Precision of reals: 8

PLUMED: Running over 1 node

PLUMED: Number of atoms: 108

PLUMED: File suffix:

PLUMED: FILE: plumed.dat

********** STACK DUMP **********

0   plumed                              0x0000000108bceeff _ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv + 63

1   ???                                 0x00007fff571b4090 0x0 + 140734654791824

******** END STACK DUMP ********

+++ Internal PLUMED error

+++ file IFile.cpp, line 111

+++ message: assertion failed do_exist, file plumed.dat cannot be found

Abort trap: 6

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

[Gareth Tribello]

Hello

The plumed.dat files are the input files for plumed.  You have to work out how to write them yourself for this tutorial by reading through the manual.  There are hints in what is written there.  If you just want to run a simplemd calculation though and get a trajectory you can just create a file called plumed.dat and the calculation should run.  When you get to things like

Create a plumed input file that calculates the average COORDINATIONNUMBER of the atoms in your system and outputs it to a file every 100 steps.

Then you will need to put stuff into the plumed.dat file in order to get it to calculate the quantities that are required.  The links here will be very useful to you.

Gareth

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[Lei Wu]

Thanks Gareth.  I wonder if it's possible to explicitly specify the input files for plumed, just like when we use gromacs that patched with plumed.

Best,

Lei

在 2015年6月27日星期六 UTC-4下午4:42:45，Gareth Tribello写道：

[gareth....@gmail.com]

Hello

I'm sorry but I don't think it is possible to give your plumed input files any name other than plumed.dat when you use simplemd. The name plumed.dat for the plumed input is hard coded into that particular md engine.

Gareth

Sent from my iPad

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