*Dear users* *I am evaluating interaction of a ligand with a protein named amyloid. I want to use 5 molecules of ligand in my simulation. I run the following commands:*
>> pdb2gmx -f bamyloid.pdb -o bamyloid.gro -p bamyloid.top -water spc then modifying the "bamyloid.gro" and adding 5 mols of ligand..... modifying "bamyloid.top" >> editconf -f bamyloid.gro -o newbox.gro -bt dodecahedron -d 1.0 >> genbox -cp newbox.gro -cs spc216.gro -p bamyloid.top -o solv.gro >> grompp -f em.mdp -c solv.gro -p bamyloid.top -o ions.tpr this is the content of md.mdp file: title = Minimization integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 energygrps = system nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz >> genion -s ions.tpr -o solv.ions.gro -p bamyloid.top -pname NA -nname CL -np 40 this is the content of bamyloid.top : ; Include forcefield parameters #include "gromos53a6.ff/forcefield.itp" ; Include chain topologies #include "bamyloid_Protein_chain_A.itp" #include "bamyloid_Protein_chain_B.itp" #include "bamyloid_Protein_chain_C.itp" #include "bamyloid_Protein_chain_D.itp" #include "bamyloid_Protein_chain_E.itp" #include "bamyloid_Protein_chain_F.itp" #include "bamyloid_Protein_chain_G.itp" #include "bamyloid_Protein_chain_H.itp" #include "bamyloid_Protein_chain_I.itp" #include "bamyloid_Protein_chain_J.itp" #include "bamyloid_Protein_chain_K.itp" #include "bamyloid_Protein_chain_L.itp" #include "bamyloid_Protein_chain_M.itp" #include "bamyloid_Protein_chain_N.itp" #include "bamyloid_Protein_chain_O.itp" #include "bamyloid_Protein_chain_P.itp" #include "bamyloid_Protein_chain_Q.itp" #include "bamyloid_Protein_chain_R.itp" #include "bamyloid_Protein_chain_S.itp" #include "bamyloid_Protein_chain_T.itp" ; Include ligand topology #include "oximeo.itp" ; Include water topology #include "gromos53a6.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos53a6.ff/ions.itp" [ system ] ; Name --- in water [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 Protein_chain_D 1 Protein_chain_E 1 Protein_chain_F 1 Protein_chain_G 1 Protein_chain_H 1 Protein_chain_I 1 Protein_chain_J 1 Protein_chain_K 1 Protein_chain_L 1 Protein_chain_M 1 Protein_chain_N 1 Protein_chain_O 1 Protein_chain_P 1 Protein_chain_Q 1 Protein_chain_R 1 Protein_chain_S 1 Protein_chain_T 1 oxm 5 SOL 17592 NA 40 >> grompp -f em-real.mdp -c solv-ions.gro -p bamyloid.top -o em.tpr this is the content of em-real.mdp: title = Minimization integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 energygrps = protein oxm nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz ***** but when I run command ">> mdrun -v deffnm em", I get the following fatal error:* Linking all bonded interactions to atoms There are 11265 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 2 The initial domain decomposition cell size is: X 0.96 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.000 nm two-body bonded interactions (-rdd) 1.000 nm multi-body bonded interactions (-rdd) 0.964 nm Making 1D domain decomposition grid 8 x 1 x 1, home cell index 0 0 0 Initiating Steepest Descents Charge group distribution at step 0: 2473 2348 2361 2395 2347 2304 2342 2377 Grid: 11 x 14 x 10 cells Started Steepest Descents on node 0 Sat May 3 05:26:27 2014 Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step Time Lambda 0 0.00000 0.00000 DD step 0 load imb.: force 4.9% ------------------------------------------------------- Program mdrun, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/mdlib/pme.c, line: 538 *Fatal error:* *80 particles communicated to PME node 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated.* *For more information and tips for troubleshooting, please check the GROMACS* *website at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>* ------------------------------------------------------- *Could anyone tell me how to solve this problem???* *your help is appreciated....* -- ********************* Dr. Hamid Irannejad (Pharm D. & PhD) Department of Medicinal Chemistry Faculty of Pharmacy Mazandaran University of Medical Sciences Sari, Iran Fax: 0098 151 3543084 Postal code: 4847116547 http://orcid.org/0000-0001-7513-6162 ************************* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.