[gmx-users] Position Restrain Problem
Anthony Cruz
acb15885 at uprm.edu
Tue Dec 20 16:17:07 CET 2005
grompp not gives any warning when reading in the topology and
coordinates. This is my topology file:
;
; File 'pzav_Top.top' was generated
; By user: acruz (1001)
; On host: tccg8
; At date: Fri Dec 16 09:48:52 2005
;
; This is your topology file
; HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR; 3 ALPHA CHAIN; HLA CLASS
II HISTOCOMPATIBILITY ANTIGEN, DRB1-1; 10 BETA CHAIN; GAG POLYPROTEIN; ENTERO
TOXIN TYPE C-3
;
; Include forcefield parameters
#include "ffG43a1.itp"
; Include chain topologies
#include "pzav_Top_A.itp"
#include "pzav_Top_C.itp"
; Include water topology
#include "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 generic topology for ions
#include "ions.itp"
[ system ]
; Name
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR; 3 ALPHA CHAIN; HLA CLASS II
HISTOCOMPATIBILITY ANTIGEN, DRB1-1; 10 BETA CHAIN; GAG POLYPROTEIN;
ENTEROTOXIN TY
PE C-3 in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_C 1
SOL 95131
NA+ 18
This is my MDP file for the position restrain:
title = SHLA CLASS II HISTOCOMPATIBILITY ANTIGEN
warnings = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 300000 ; total 600 ps.
nstcomm = 1
; Output Control
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstenergy = 500
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
pbc = xyz
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc_grps = Protein SOL NA+
ref_t = 298 298 298
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 298 K.
gen_vel = yes
gen_temp = 298.0
gen_seed = 173529
The only thing is that I have only one protein group and in the topology I
have 2 itp one for the protein (2 units) and another for the peptide. I need
to split the Protein group in two?
Anthony
On Monday 19 December 2005 2:01 pm, Andrea C. Vaiana wrote:
> I had a similar problem and it turned out that in my coordinate file
> atoms were ordered differently than in the topology file...
> check if grompp gives a warning when reading in the topology and
> coordinates.
> Andrea
>
> On Dec 19, 2005, at 1:08 PM, Anthony Cruz wrote:
> > Hi users:
> > I am trying to run a simulation of the interaction between a
> > protein that have
> > two units and a small peptide. First I have the pdb file of the
> > protein (2
> > subunits) and the peptide. I use the -merge option of pdb2gmx to
> > merge the
> > two protein subunits in one topology and the peptide in other
> > topology but
> > all in the same .gro. I run the energy minimization without problem
> > but it
> > end too rapidly:
> >
> > Energies (kJ/mol)
> > G96Bond G96Angle Proper Dih. Improper
> > Dih. LJ-14
> > 5.04580e+02 1.64344e+03 1.89068e+03 2.77582e+02
> > 2.00071e+03
> > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR)
> > Coulomb (LR)
> > 4.12043e+04 7.06859e+05 -1.90071e+04 -4.29975e+06
> > -4.75686e+05
> > Potential Kinetic En. Total Energy Temperature
> > Pressure (bar)
> > -4.04006e+06 0.00000e+00 0.00000e+00 0.00000e+00
> > 0.00000e+00
> >
> > Step Time Lambda
> > 27 27.00000 0.00000
> >
> > Step Time Lambda
> > 28 28.00000 0.00000
> >
> > Step Time Lambda
> > 29 29.00000 0.00000
> >
> >
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 100
> >
> > Double precision normally gives you higher accuracy.
> > You might need to increase your constraint accuracy, or turn
> > off constraints alltogether (set constraints = none in mdp file)
> >
> > Steepest Descents converged to machine precision in 30 steps,
> > but did not reach the requested Fmax < 100.
> > Potential Energy = -4.0400605e+06
> > Maximum force = 2.5371721e+03 on atom 195774
> > Norm of force = 5.4543950e+05
> >
> > When I try to run the position restrain dynamics the process end
> > abruptly.
> > With this output from the log file :
> >
> > Initializing LINear Constraint Solver
> > number of constraints is 3992
> > average number of constraints coupled to one constraint is 2.9
> >
> > Rel. Constraint Deviation: Max between atoms RMS
> > Before LINCS 0.040178 2221 2222 0.006943
> > After LINCS 0.000491 1144 1146 0.000052
> >
> > Going to use C-settle (4728 waters)
> > wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra =
> > 0.00645837
> > rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1
> >
> > Constraining the coordinates at t0-dt (step -1)
> > Rel. Constraint Deviation: Max between atoms RMS
> > Before LINCS 0.093162 2933 2934 0.016557
> > After LINCS 0.000218 1271 1273 0.000034
> >
> > Started mdrun on node 0 Mon Dec 19 09:31:45 2005
> > Initial temperature: 298.48 K
> > Step Time Lambda
> > 0 0.00000 0.00000
> >
> > Grid: 20 x 20 x 20 cells
> > Rel. Constraint Deviation: Max between atoms RMS
> > Before LINCS 0.066290 2460 2461 0.005114
> > After LINCS 0.000133 1144 1146 0.000015
> >
> > Energies (kJ/mol)
> > G96Angle Proper Dih. Improper Dih. LJ-14
> > Coulomb-14
> > 2.01626e+03 1.90234e+03 3.07489e+02 2.05943e+03
> > 4.13328e+04
> > LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
> > Position Rest.
> > 7.08229e+05 -1.90024e+04 -4.30085e+06 -5.03389e+05
> > 1.49338e+06
> > Potential Kinetic En. Total Energy Temperature
> > Pressure (bar)
> > -2.57402e+06 7.21568e+05 -1.85245e+06 2.99867e+02
> > -1.16469e+03
> >
> >
> > t = 0.020 ps: Water molecule starting at atom 3923 can not be settled.
> > Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> > previous and current coordinates
> >
> > t = 0.036 ps: Water molecule starting at atom 7658 can not be settled.
> > Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> > previous and current coordinates
> >
> > t = 0.038 ps: Water molecule starting at atom 7703 can not be settled.
> > Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> > previous and current coordinates
> >
> > t = 0.040 ps: Water molecule starting at atom 8420 can not be settled.
> > Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> > previous and current coordinates
> >
> > t = 0.042 ps: Water molecule starting at atom 7724 can not be settled.
> > Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> > previous and current coordinates
> >
> >
> > And the following output from the pbs errors file:
> >
> > starting mdrun 'HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR'
> > 300000 steps, 600.0 ps.
> >
> > step 0
> > Wrote pdb files with previous and current coordinates
> > step 10, will finish at Wed May 31 14:12:32 2006
> > Wrote pdb files with previous and current coordinates
> >
> > Back Off! I just backed up step17.pdb to ./#step17.pdb.1#
> > Wrote pdb files with previous and current coordinates
> >
> > Back Off! I just backed up step18.pdb to ./#step18.pdb.1#
> > Sorry couldn't backup step18.pdb to ./#step18.pdb.1#
> >
> > Back Off! I just backed up step19.pdb to ./#step19.pdb.1#
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> >
> > Back Off! I just backed up step19.pdb to ./#step19.pdb.2#
> > Wrote pdb files with previous and current coordinates
> > step 20, will finish at Sat Apr 7 06:34:59 2007
> >
> > Back Off! I just backed up step20.pdb to ./#step20.pdb.1#
> > Sorry couldn't backup step20.pdb to ./#step20.pdb.1#
> >
> > Back Off! I just backed up step21.pdb to ./#step21.pdb.1#
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > MPI: On host caffenero.hpcf.upr.edu,
> > Program /usr/local/gromacs/ia64-unknown-linux-gnu/bin/mdrun_mpi,
> > Rank 15,
> > Process 31770 received signal SIGSEGV(11)
> >
> >
> > MPI: --------stack traceback-------
> > sh: line 1: idb: command not found
> >
> > MPI: -----stack traceback ends-----
> > MPI: On host caffenero.hpcf.upr.edu,
> > Program /usr/local/gromacs/ia64-unknown-linux-gnu/bin/mdrun_mpi,
> > Rank 15,
> > Process 31770: Dumping core on signal SIGSEG
> > V(11) into directory /home/acruz/asv.31738
> > MPI: MPI_COMM_WORLD rank 15 has terminated without calling
> > MPI_Finalize()
> > MPI: aborting job
> > MPI: Received signal 11
> >
> > What could be the problem???
> > _______________________________________________
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