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 ------------------------------------------------------- -- View this message in context: http://gromacs.5086.n6.nabble.com/Problem-with-minimizing-the-energy-of-the-solvated-system-tp4999121.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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