[gmx-users] problem in using more than one molecule of a ligand in simulation

[Justin Lemkul]

On 5/2/14, 3:19 AM, Hamid Irannejad wrote:
> *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???*
>

Immediate failure during EM means your coordinates are catastrophically bad in 
some way.  Check your inputs carefully.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================