fps.lp error, WRAPAROUND, NOPBC not helping

[Andrej Tekel]

Dear PLUMED users,

I have been trying funnel metadynamics, but I can not get rid of the error that is already mentioned several times in this group : ERROR: the system is looking for a value outside the grid along the 0 (fps.lp) index!  

I have already tried tricks mentioned in previous answers to this question, using NOPBC on fps, WRAPAROUND ligand to protein, some tweaks with reference structure...so far nothing worked in my case. Any help is appreciated, thank you.

Best,

Andrej

Here is my plumed.dat:

protein: GROUP ATOMS=1-1568
ligand: GROUP ATOMS=1569-1607
anchor_atom: GROUP ATOMS=140

WHOLEMOLECULES ENTITY0=protein

WRAPAROUND ATOMS=ligand AROUND=anchor_atom GROUPBY=39

lig: COM ATOMS=1569-1607  
d1: DISTANCE ATOMS=1577,lig  
fps: FUNNEL_PS LIGAND=lig REFERENCE=str.pdb ANCHOR=140 POINTS=-0.0503,1.0548,0.4248,-0.3909,1.5901,1.1295 NOPBC  

FUNNEL ARG=fps.lp,fps.ld ZCC=0.7 ALPHA=1.00 RCYL=0.15 MINS=0 MAXS=5.3 KAPPA=35100 NBINS=500 NBINZ=500 FILE=BIAS LABEL=funnel
 
METAD ARG=d1 SIGMA=0.01 HEIGHT=2.0 PACE=500 TEMP=300 BIASFACTOR=20 LABEL=metad GRID_MIN=0 GRID_MAX=6.0 CALC_RCT RCT_USTRIDE=1

LOWER_WALLS ARG=fps.lp AT=0 KAPPA=35100 EXP=2 OFFSET=0 LABEL=lwall
UPPER_WALLS ARG=fps.lp AT=3 KAPPA=35100 EXP=2 OFFSET=0 LABEL=uwall
UPPER_WALLS ARG=d1 AT=3.5 KAPPA=35100 EXP=2 OFFSET=0 LABEL=distwall

PRINT STRIDE=500 ARG=* FILE=COLVAR

[Gareth Tribello]

Make GRID_MAX for the metadynamics larger.  You might also want to consider putting a wall on d1 to prevent the ligand from moving very far from the protein.

Good luck

Gareth

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[Andrej Tekel]

Hello,

Thank you, but I think I have already upper wall on protein ligand distance (in .dat mentioned above UPPER_WALLS ARG=d1 AT=3.5 KAPPA=35100 EXP=2 OFFSET=0 LABEL=distwall). Please correct me if I am wrong. I am always checking colvar file and everything seems to be within range that is defined, not even close to the boundaries.

Best,

Andrej

čt 25. 3. 2021 v 19:03 odesílatel Gareth Tribello <gareth....@gmail.com> napsal:

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[Stefano Raniolo]

Dear Andrej Tekel,

I am sorry that you are finding difficulties with the Funnel. 

The solution changes depending if this happen at the beginning of the simulation or after some steps.

If it is at the beginning, please check the str.pdb file. Are there only target atoms (protein only)? Are the atom serials renumbered?

If you used VMD and you choose only a selection of atoms it is possible that serials are different from the ones in your simulation. In this case, the alignment inside FUNNEL_PS will misplace the funnel and the ligand will appear outside from the grid of BIAS.

As for exiting the grid after some steps, the only solution is WRAP AROUND or WHOLEMOLECULES (also having ligand atoms in str.pdb can create problems). 

The "combo" with NOPBC on FUNNEL_PS is generally suggested if you provide a customised selection of atoms on WHOLEMOLECULES. The order would be the following: <all atoms in str.pdb>,140,1569-1607. This holds true only if ANCHOR has been defined as the closest target atom with respect to the ligand position (otherwise it will not help). This should work fine if your target is globular, otherwise an ad hoc declaration might be necessary for elongated molecules and oligomeric proteins.

Hope it helps.

Other possible solutions would require to observe the values of CVs, walls, etc. before the crash. In case you need further help you can contact me via PM. I have experience in debugging Funnel-related systems.

Best regards,

Stefano Raniolo

[rubina noor]

hello plumed users

i am trying to run funnel metadynamics simulation and have used several ways to perform it but at each time I get following error and am not able to solve  

terminate called after throwing an instance of 'PLMD::ExceptionError'
 what():   
+++ PLUMED error
+++ at Grid.cpp:169, function PLMD::GridBase::index_t PLMD::GridBase::getIndex(const std::vector<unsigned int>&) const
+++ message follows +++
ERROR: the system is looking for a value outside the grid along the 1 (fps.ld) index!

Program received signal SIGABRT: Process abort signal.

I am looking forward to hear from you 
 
Thank you

With best regards

Rubina