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Error in metadynamics run with plumed
- Imamul
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4 years 7 months ago #8245
by Imamul
Error in metadynamics run with plumed was created by Imamul
Hi All,
I am novice in free energy calculation with metadynamics. I tried to calculate the free energy using the below plumed.dat file of a biolocal multicomplex system containing lipids, cholesterol, and protein in the form of monolayers separated by a layer of water. Plumed.dat file
"d1: DENSITY SPECIES=1840-6015:12,1849-6015:12 LOWMEM
COM ATOMS=1,1607 LABEL=com1
cont: DISTANCE_FROM_CONTOUR ATOM=com1 DATA=d1 BANDWIDTH=3.0,3.0,3.0 DIR=z CONTOUR=0.42
METAD ...
ARG=cont
SIGMA=0.7
HEIGHT=1.8
BIASFACTOR=10
PACE=500
LABEL=mm
GRID_MIN=-10
GRID_MAX=150
GRID_BIN=115000
ADAPTIVE=GEOM
SIGMA_MIN=0.05
SIGMA_MAX=6.00
TEMP=310
... METAD
UPPER_WALLS ARG=cont AT=50.0 KAPPA=1.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall
c1: COM ATOMS=1840-6015:12,1849-6015:12
d3: DISTANCE ATOMS=c1,com1 NOPBC COMPONENTS
PRINT ARG=cont.*,mm.bias STRIDE=20 FILE=COLVAR
PRINT ARG=d3.* STRIDE=20 FILE=colvar_com"
The whole system is placed in a priodic box and a NP is placed above on monolayer. The NP freely move towards the monolayer during the simulation with plumed. Keeping the similarities with the following paper
Using Intrinsic Surfaces To Calculate the "Free-Energy Change When
Nanoparticles Adsorb on Membranes"
https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b03661
I wanna calculate the perpendicular distance between the NP and the monolayer surface. Each monolayer contains
NP 1
Protein_A 4
DPPC 244
POPG 104
CHOL 32
What will be the approximate density contour, width of Gausian, height of the Gausian?
I have fine-tuned the plumed input parameters (please see plumed.dat) e.g., the Gausian width, height, and Baisfactor. The NP freely interact with the monolayer lipids-proteins, the simulation suddenly stopped after 10 ns with an error below (please see bellow). I am simulating the system using Martini force field.
"+++ Internal PLUMED error
+++ file tools/../../tools/Brent1DRootSearch.h, line 78
+++ message: input points do not bracket root
/var/spool/pbs/mom_priv/jobs/230257.hpcnode0.SC: line 21: 92762 Aborted"
gmx mdrun -nt $NCPUS -ntomp $NCPUS -ntmpi 0 -deffnm pro1 -plumed plumed.dat
Please suggest me about the things that I need in these situation.
Thanks in advace.
Regards
Sheikh Imamul
I am novice in free energy calculation with metadynamics. I tried to calculate the free energy using the below plumed.dat file of a biolocal multicomplex system containing lipids, cholesterol, and protein in the form of monolayers separated by a layer of water. Plumed.dat file
"d1: DENSITY SPECIES=1840-6015:12,1849-6015:12 LOWMEM
COM ATOMS=1,1607 LABEL=com1
cont: DISTANCE_FROM_CONTOUR ATOM=com1 DATA=d1 BANDWIDTH=3.0,3.0,3.0 DIR=z CONTOUR=0.42
METAD ...
ARG=cont
SIGMA=0.7
HEIGHT=1.8
BIASFACTOR=10
PACE=500
LABEL=mm
GRID_MIN=-10
GRID_MAX=150
GRID_BIN=115000
ADAPTIVE=GEOM
SIGMA_MIN=0.05
SIGMA_MAX=6.00
TEMP=310
... METAD
UPPER_WALLS ARG=cont AT=50.0 KAPPA=1.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall
c1: COM ATOMS=1840-6015:12,1849-6015:12
d3: DISTANCE ATOMS=c1,com1 NOPBC COMPONENTS
PRINT ARG=cont.*,mm.bias STRIDE=20 FILE=COLVAR
PRINT ARG=d3.* STRIDE=20 FILE=colvar_com"
The whole system is placed in a priodic box and a NP is placed above on monolayer. The NP freely move towards the monolayer during the simulation with plumed. Keeping the similarities with the following paper
Using Intrinsic Surfaces To Calculate the "Free-Energy Change When
Nanoparticles Adsorb on Membranes"
https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b03661
I wanna calculate the perpendicular distance between the NP and the monolayer surface. Each monolayer contains
NP 1
Protein_A 4
DPPC 244
POPG 104
CHOL 32
What will be the approximate density contour, width of Gausian, height of the Gausian?
I have fine-tuned the plumed input parameters (please see plumed.dat) e.g., the Gausian width, height, and Baisfactor. The NP freely interact with the monolayer lipids-proteins, the simulation suddenly stopped after 10 ns with an error below (please see bellow). I am simulating the system using Martini force field.
"+++ Internal PLUMED error
+++ file tools/../../tools/Brent1DRootSearch.h, line 78
+++ message: input points do not bracket root
/var/spool/pbs/mom_priv/jobs/230257.hpcnode0.SC: line 21: 92762 Aborted"
gmx mdrun -nt $NCPUS -ntomp $NCPUS -ntmpi 0 -deffnm pro1 -plumed plumed.dat
Please suggest me about the things that I need in these situation.
Thanks in advace.
Regards
Sheikh Imamul
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- riccardo
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4 years 7 months ago #8247
by riccardo
Replied by riccardo on topic Error in metadynamics run with plumed
I think that this is a question best-suited for the PLUMED forum/people.
We do have a metadynamics tutorial with Martini, though. You may take a look: cgmartini.nl/index.php/tutorials-general...on-gmx5/metadynamics .
We do have a metadynamics tutorial with Martini, though. You may take a look: cgmartini.nl/index.php/tutorials-general...on-gmx5/metadynamics .
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