Problem with the AROUND keyword

[jkenne...@gmail.com]

Hello,

I am attempting to use GROMACS5.0.4 with PLUMED2.1.0 using the AROUND keyword, and having difficulties. What I want to do is to compare the solvent density "above" (higher z) and "below" (lower z) a specific site (the center of mass of two Asp residues). Here is what my code looks like; there is some extraneous stuff going on here, so I've marked the relevant lines by putting spaces between them and the rest of the block:

WHOLEMOLECULES STRIDE=1 ENTITY0=1-5859 ENTITY1=5860-38473
COM ATOMS=2377-2401 LABEL=COMAsps
COM ATOMS=10-1127,3273-4253 LABEL=COMdimer
COM ATOMS=5860-38473 LABEL=COMlipids
pdimer: POSITION ATOM=COMdimer
plipids: POSITION ATOM=COMlipids
pAsps: POSITION ATOM=COMAsps
COMBINE LABEL=ddimer ARG=pdimer.z,plipids.z COEFFICIENTS=1,-1 PERIODIC=-4.556955,4.556955
RESTRAINT ARG=ddimer AT=-0.18 KAPPA=250.0 LABEL=restddimer

DENSITY SPECIES=38474-81875:3,81965-87335:3 LABEL=rhoOw

AROUND ATOM=COMAsps DATA=rhoOw XLOWER=-1.20 XUPPER=1.20 YLOWER=-1.20 YUPPER=1.20 ZLOWER=0.0 ZUPPER=1.50 SIGMA=0.1 LABEL=rhoup

AROUND ATOM=COMAsps DATA=rhoOw XLOWER=-1.20 XUPPER=1.20 YLOWER=-1.20 YUPPER=1.20 ZLOWER=-1.50 ZUPPER=0.0 SIGMA=0.1 LABEL=rhodown

COMBINE LABEL=drho ARG=rhoup,rhodown COEFFICIENTS=1,-1 PERIODIC=NO

METAD ARG=drho SIGMA=0.04 HEIGHT=0.4 PACE=3000 LABEL=metawat FILE=HILLS_Asp156
PRINT ARG=drho,metawat.bias,ddimer,restddimer.bias STRIDE=500 FILE=COLVAR_Asp156

My issue is this: The example in the manual seems to indicate that I should be using 'ARG=rhoOw', but if I do that, I get the message:

+++ Internal PLUMED error
+++ file Action.cpp, line 198
+++ message: ERROR in input to action AROUND with label rhoup : keyword DATA is compulsory for this action

However, switching to the version above instead gives this error:

+++ Internal PLUMED error
+++ file vesselbase/../../vesselbase/ActionWithVessel.h, line 205

(There's a stack dump with a bunch more information that I can copy if desired, but it doesn't seem too helpful to me.) So, before I put a bunch of work into validating that my PLUMED installation is functioning correctly (linked to all the right libraries, etc.), I was hoping to verify that there wasn't a problem with my metadynamics input (particularly the lines beginning with 'AROUND').

Thanks in advance for any help you may provide.

--Josh

[Gareth Tribello]

Hello

I’m sorry but that example uses the wrong input syntax.  I will change it now in order to prevent confusion in the past.  You definitely need to use DATA rather than ARG in around.  

The error that you are getting is a bit strange.  Can you look in the file src/multicolvar/ActionVolume.h and check if there is a function defined as follows:

void applyBridgeForces( const std::vector<double>& bb );

It is there in the latest version of v2.1 but I am not sure what version of the code you have.  Perhaps there is a bug in an old version that you are using.   This stuff should work if the master version of plumed, which you can download from here:

https://github.com/plumed/plumed2

As we have been using these features for some stuff that we have been doing.  It should also work with version 2.1 as the correct code seems to be there.  There was a bug in this at some stage though that we fixed.  Maybe you have a version from before the bug was fixed.

I hope this helps

Gareth

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[jkenne...@gmail.com]

OK. I am using a PLUMED module installed on my cluster by the computing center on my campus; I will contact them about this problem and see if we can get to the bottom of this. (I wanted to try to make sure there wasn't a problem with my PLUMED input before I did that.) If I think the solution is likely to be of general use (rather than being a quirky installation problem), I'll write back.

Thanks,

Josh