[gmx-users] Problem with minimizing the energy of the solvated system
jonas87
jonas_dehairs at hotmail.com
Thu Jul 5 21:15:44 CEST 2012
Hi,
I'm new to gromacs, after following a few lectures on MD decided to try out
this gromacs tutorial:
http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html
http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html
I can get till the section "Energy minimization of the solvated system" but
then I get an error. See input output bellow.
I used protein 1XYW.pdb and followed the tutorial exactly. Bolded the input
for reading convenience.
*pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh*
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
NOTE 1 [file protein.top, line 7580]:
System has non-zero total charge: -1.999999
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 111 Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 3603.00
NOTE 2 [file minim.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
Largest charge group radii for Van der Waals: 0.249, 0.247 nm
Largest charge group radii for Coulomb: 0.249, 0.247 nm
This run will generate roughly 1 Mb of data
There were 2 notes
*mdrun -v -deffnm protein-EM-vacuum -c protein-EM-vacuum.pdb -pd
*
Getting Loaded...
Reading file protein-EM-vacuum.tpr, VERSION 4.5.5 (single precision)
Starting 4 threads
Loaded with Money
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 500
Step= 0, Dmax= 1.0e-02 nm, Epot= -5.95507e+03 Fmax= 6.00562e+03, atom=
1200
Step= 1, Dmax= 1.0e-02 nm, Epot= -6.89393e+03 Fmax= 5.80491e+03, atom=
1200
Step= 3, Dmax= 6.0e-03 nm, Epot= -7.25585e+03 Fmax= 1.34980e+03, atom=
8530
Step= 5, Dmax= 3.6e-03 nm, Epot= -7.38989e+03 Fmax= 2.35146e+03, atom=
1200
Step= 6, Dmax= 4.3e-03 nm, Epot= -7.41163e+03 Fmax= 2.75876e+03, atom=
1200
Step= 8, Dmax= 2.6e-03 nm, Epot= -7.55085e+03 Fmax= 9.78988e+02, atom=
8530
Step= 9, Dmax= 3.1e-03 nm, Epot= -7.57962e+03 Fmax= 2.02528e+03, atom=
1014
Step= 11, Dmax= 1.9e-03 nm, Epot= -7.66238e+03 Fmax= 8.21663e+02, atom=
5484
Step= 12, Dmax= 2.2e-03 nm, Epot= -7.68826e+03 Fmax= 1.51218e+03, atom=
1014
Step= 14, Dmax= 1.3e-03 nm, Epot= -7.73520e+03 Fmax= 7.89052e+02, atom=
5484
Step= 15, Dmax= 1.6e-03 nm, Epot= -7.76507e+03 Fmax= 7.71421e+02, atom=
548
Step= 16, Dmax= 1.9e-03 nm, Epot= -7.77461e+03 Fmax= 1.60933e+03, atom=
232
Step= 17, Dmax= 2.3e-03 nm, Epot= -7.79399e+03 Fmax= 1.67008e+03, atom=
232
Step= 19, Dmax= 1.4e-03 nm, Epot= -7.83819e+03 Fmax= 7.34264e+02, atom=
548
Step= 20, Dmax= 1.7e-03 nm, Epot= -7.86427e+03 Fmax= 7.18507e+02, atom=
548
Step= 21, Dmax= 2.0e-03 nm, Epot= -7.86821e+03 Fmax= 1.81121e+03, atom=
495
Step= 22, Dmax= 2.4e-03 nm, Epot= -7.89209e+03 Fmax= 1.62537e+03, atom=
495
Step= 24, Dmax= 1.4e-03 nm, Epot= -7.92346e+03 Fmax= 6.81625e+02, atom=
548
Step= 25, Dmax= 1.7e-03 nm, Epot= -7.94277e+03 Fmax= 1.06912e+03, atom=
495
Step= 26, Dmax= 2.1e-03 nm, Epot= -7.94602e+03 Fmax= 1.81658e+03, atom=
495
Step= 27, Dmax= 2.5e-03 nm, Epot= -7.96312e+03 Fmax= 1.74561e+03, atom=
495
Step= 29, Dmax= 1.5e-03 nm, Epot= -7.99085e+03 Fmax= 6.34520e+02, atom=
548
Step= 30, Dmax= 1.8e-03 nm, Epot= -8.01026e+03 Fmax= 1.10715e+03, atom=
495
Step= 31, Dmax= 2.2e-03 nm, Epot= -8.01349e+03 Fmax= 1.89322e+03, atom=
495
Step= 32, Dmax= 2.6e-03 nm, Epot= -8.02849e+03 Fmax= 1.79914e+03, atom=
495
Step= 33, Dmax= 3.1e-03 nm, Epot= -8.16573e+03 Fmax= 2.54108e+03, atom=
495
Step= 34, Dmax= 3.7e-03 nm, Epot= -8.17359e+03 Fmax= 2.76266e+03, atom=
495
Step= 36, Dmax= 2.2e-03 nm, Epot= -8.21648e+03 Fmax= 5.69522e+02, atom=
548
Step= 40, Dmax= 3.4e-04 nm, Epot= -8.22184e+03 Fmax= 5.66199e+02, atom=
548
Step= 43, Dmax= 1.0e-04 nm, Epot= -8.22327e+03 Fmax= 5.65172e+02, atom=
548
Step= 47, Dmax= 1.5e-05 nm, Epot= -8.22348e+03 Fmax= 5.65018e+02, atom=
548
Step= 49, Dmax= 9.1e-06 nm, Epot= -8.22360e+03 Fmax= 5.64925e+02, atom=
548
Step= 53, Dmax= 1.4e-06 nm, Epot= -8.22362e+03 Fmax= 5.64911e+02, atom=
548
Step= 54, Dmax= 1.6e-06 nm, Epot= -8.08422e+03 Fmax= 5.64895e+02, atom=
548
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 55 steps,
but did not reach the requested Fmax < 1.
Potential Energy = -8.2236152e+03
Maximum force = 5.6491138e+02 on atom 548
Norm of force = 7.9913132e+01
*editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
1.0 *
Read 1202 atoms
No velocities found
system size : 5.245 4.320 2.507 (nm)
diameter : 5.532 (nm)
center : 0.010 0.047 -0.011 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 5.640 5.602 2.674 (nm)
new center : 5.649 5.649 2.663 (nm)
new box vectors : 7.532 7.532 7.532 (nm)
new box angles : 60.00 60.00 90.00 (degrees)
new box volume : 302.20 (nm^3)
*genbox -cp protein-PBC.gro -cs spc216.gro -p protein.top -o
protein-water.pdb
*
Reading solute configuration
MAJOR PRION PROTEIN
Containing 1202 atoms in 111 residues
Initialising van der waals distances...
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
from the correct mass and radius of the atom type.
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 5x5x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 16200 residues
Calculating Overlap...
box_margin = 0.315
Removed 14616 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
System total charge: 0.000
Grid: 19 x 19 x 14 cells
Successfully made neighbourlist
nri = 70460, nrj = 2270425
Checking Protein-Solvent overlap: tested 22103 pairs, removed 1896 atoms.
Checking Solvent-Solvent overlap: tested 331095 pairs, removed 4338 atoms.
Added 9250 molecules
Generated solvent containing 27750 atoms in 9250 residues
Writing generated configuration to protein-water.pdb
Back Off! I just backed up protein-water.pdb to ./#protein-water.pdb.1#
MAJOR PRION PROTEIN
Output configuration contains 28952 atoms in 9361 residues
Volume : 302.196 (nm^3)
Density : 1007.94 (g/l)
Number of SOL molecules: 9250
Processing topology
*grompp -v -f minim.mdp -c protein-water.pdb -p protein.top -o
protein-water.tpr
*
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file protein.top, line 7581]:
System has non-zero total charge: -1.999999
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
There are: 111 Protein residues
There are: 9250 Water residues
Analysing Protein...
Making dummy/rest group for T-Coupling containing 28952 elements
Making dummy/rest group for Acceleration containing 28952 elements
Making dummy/rest group for Freeze containing 28952 elements
Making dummy/rest group for VCM containing 28952 elements
Number of degrees of freedom in T-Coupling group rest is 86853.00
Making dummy/rest group for User1 containing 28952 elements
Making dummy/rest group for User2 containing 28952 elements
Making dummy/rest group for XTC containing 28952 elements
Making dummy/rest group for Or. Res. Fit containing 28952 elements
Making dummy/rest group for QMMM containing 28952 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): System
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
NOTE 2 [file minim.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
Largest charge group radii for Van der Waals: 0.248, 0.248 nm
Largest charge group radii for Coulomb: 0.248, 0.248 nm
This run will generate roughly 7 Mb of data
writing run input file...
There were 2 notes
*genion -s protein-water.tpr -o protein-solvated.pdb -conc 0.15 -neutral
-pname NA -nname CL *
Reading file protein-water.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 29 NA ions and 27 CL ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 28952 elements
Group 1 ( Protein) has 1202 elements
Group 2 ( Protein-H) has 919 elements
Group 3 ( C-alpha) has 111 elements
Group 4 ( Backbone) has 333 elements
Group 5 ( MainChain) has 445 elements
Group 6 ( MainChain+Cb) has 548 elements
Group 7 ( MainChain+H) has 555 elements
Group 8 ( SideChain) has 647 elements
Group 9 ( SideChain-H) has 474 elements
Group 10 ( Prot-Masses) has 1202 elements
Group 11 ( non-Protein) has 27750 elements
Group 12 ( Water) has 27750 elements
Group 13 ( SOL) has 27750 elements
Group 14 ( non-Water) has 1202 elements
Select a group: 13
Selected 13: 'SOL'
Number of (3-atomic) solvent molecules: 9250
Replacing solvent molecule 1085 (atom 4457) with NA
Replacing solvent molecule 7008 (atom 22226) with NA
Replacing solvent molecule 4515 (atom 14747) with NA
Replacing solvent molecule 7826 (atom 24680) with CL
Replacing solvent molecule 3080 (atom 10442) with NA
Replacing solvent molecule 1481 (atom 5645) with CL
Replacing solvent molecule 3571 (atom 11915) with NA
Replacing solvent molecule 8196 (atom 25790) with CL
Replacing solvent molecule 3644 (atom 12134) with NA
Replacing solvent molecule 6065 (atom 19397) with CL
Replacing solvent molecule 4947 (atom 16043) with NA
Replacing solvent molecule 6570 (atom 20912) with CL
Replacing solvent molecule 3755 (atom 12467) with NA
Replacing solvent molecule 3625 (atom 12077) with CL
Replacing solvent molecule 2761 (atom 9485) with NA
Replacing solvent molecule 756 (atom 3470) with CL
Replacing solvent molecule 2599 (atom 8999) with NA
Replacing solvent molecule 4701 (atom 15305) with CL
Replacing solvent molecule 3796 (atom 12590) with NA
Replacing solvent molecule 1313 (atom 5141) with CL
Replacing solvent molecule 1770 (atom 6512) with NA
Replacing solvent molecule 1883 (atom 6851) with CL
Replacing solvent molecule 5272 (atom 17018) with NA
Replacing solvent molecule 5703 (atom 18311) with CL
Replacing solvent molecule 7440 (atom 23522) with NA
Replacing solvent molecule 1047 (atom 4343) with CL
Replacing solvent molecule 484 (atom 2654) with NA
Replacing solvent molecule 5004 (atom 16214) with CL
Replacing solvent molecule 6501 (atom 20705) with NA
Replacing solvent molecule 3801 (atom 12605) with CL
Replacing solvent molecule 2090 (atom 7472) with NA
Replacing solvent molecule 1527 (atom 5783) with CL
Replacing solvent molecule 5034 (atom 16304) with NA
Replacing solvent molecule 8614 (atom 27044) with CL
Replacing solvent molecule 480 (atom 2642) with NA
Replacing solvent molecule 2654 (atom 9164) with CL
Replacing solvent molecule 1870 (atom 6812) with NA
Replacing solvent molecule 3236 (atom 10910) with CL
Replacing solvent molecule 3537 (atom 11813) with NA
Replacing solvent molecule 5521 (atom 17765) with CL
Replacing solvent molecule 3462 (atom 11588) with NA
Replacing solvent molecule 2578 (atom 8936) with CL
Replacing solvent molecule 6351 (atom 20255) with NA
Replacing solvent molecule 3224 (atom 10874) with CL
Replacing solvent molecule 56 (atom 1370) with NA
Replacing solvent molecule 4088 (atom 13466) with CL
Replacing solvent molecule 227 (atom 1883) with NA
Replacing solvent molecule 7726 (atom 24380) with CL
Replacing solvent molecule 8465 (atom 26597) with NA
Replacing solvent molecule 6618 (atom 21056) with CL
Replacing solvent molecule 1171 (atom 4715) with NA
Replacing solvent molecule 168 (atom 1706) with CL
Replacing solvent molecule 513 (atom 2741) with NA
Replacing solvent molecule 2389 (atom 8369) with CL
Replacing solvent molecule 2528 (atom 8786) with NA
Replacing solvent molecule 6363 (atom 20291) with CL
*
protein.top → Edit file and decrease the number of solvent molecules to
9194. Also add a line specifying the number of NA ions and a line specifying
the amount of CL:
[ molecules ]
; Compound #mols
Protein_chain_A 1
SOL 9194
NA 29
CL 27*
*
Edit the file minim.mdp and change the line pbc = no to pbc = xyz
grompp -v -f minim.mdp -c protein-solvated.pdb -p protein.top -o
protein-EM-solvated.tpr *
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
Excluding 1 bonded neighbours molecule type 'CL'
processing coordinates...
double-checking input for internal consistency...
ERROR 1 [file protein.top, line 7583]:
ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist.
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
1372
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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