[gmx-users] Gromacs 4.6 & 4.5.3 qualitative differences & 4.6 instability in polarizable force field vacuum/liquid mixture interface simulations
David van der Spoel
spoel at xray.bmc.uu.se
Sat Nov 2 19:52:03 CET 2013
On 2013-11-02 18:38, ploetz wrote:
> Dear Gromacs Users,
Please start a redmine.gromacs.org issue and assign it to me, but try to
simplify the system as much as possible. You can cut and paste all the
information to the redmine issue.
>
> I am trying to simulate a system consisting of a vacuum/condensed phase
> interface in which a 6x6x12nm condensed phase region is flanked on both ends
> (in the z-dimension) by a 6x6x12nm vacuum region to form overall box
> dimensions of 6x6x36 nm. The system is a binary liquid mixture of methanol
> (0.125 mole fraction methanol) in water using a polarizable (charge on a
> spring) force field (COS/M methanol and COS/G2 water) at 300K and 1bar. The
> system is stable in Gromacs 4.5.3; however, mdrun gives a segmentation fault
> in Gromacs 4.6 when attempting to do dynamics (energy minimization completes
> with no apparent problems). If I remove the vacuum region, mdrun works. If I
> incrementally add 2 Angstroms to the z-dimension until I reached a vacuum
> region of 34 Angstroms total (17 Angstroms on both sides of the condensed
> phase region) and try to simulate these systems, mdrun works every time.
> When I reach 36 Angstroms, the segmentation fault re-appears. Although not
> the system I am actually interested in, I did some simulations using Gromacs
> 4.6 with the 34 Angstrom vacuum region system and observed an undulating and
> very turbulant "vacuum"/condensed phase interface in which a column of
> water/methanol mixture came out of the condensed phase region to connect the
> two interfaces. Also, the center of mass motion of the system appeared to
> not have been removed. In contrast, using Gromacs 4.5.3, the interface is
> not undulating, but is "calm" and qualitatively planar, no column forms to
> connect the interfaces, and there is no problem with the center of mass
> motion removal. Some of the molecules do enter the "vacuum" region when
> running with 4.5.3, but this appears to be due to the movement of individual
> molecules, not a collective motion of many molecules. This system runs fine
> with a non-polarizable force field in Gromacs 4.6.
>
> I have also compared several properties (using g_energy) of the bulk system
> (no vacuum region) using Gromacs 4.6 and 4.5.3 and they are not the same for
> the polarizable force field, but they are the same for the non-polarizable
> force field. Specifically, with the polarizable force field, the LJ(SR)
> energy is more positive with 4.6, the LJ(LR) energy is more negative with
> 4.6, the Coulomb(SR) energy is more negative with 4.6, the Could. recip.
> energy is more negative with 4.6, the polarization energy is more positive
> with 4.6, the potential energy is more negative in 4.6, the average kinetic
> energy (and temperature) is the same but the fluctuations are greater in
> 4.6, the total energy is more negative in 4.6, the pressure looks fine, and
> the volume looks fine. Where I've noted differences, these are all
> statistically significant differences.
>
> I would like to know if I can just use 4.5.3 and assume the differences
> between the results of 4.5.3 and 4.6 are due to some problem in 4.6. I am
> using all the same input files and commands with both versions, only
> different executables. I ran the regression tests for 4.6 when I installed
> it, and passed them all.
>
> Sincerely,
>
> Elizabeth
>
> -----
> ADDITIONAL DETAILS:
> Below is where the problem appears for the interface system when z-dimension
> of the vacuum region is >= 36 Angstroms total. eq4 is my first attempt at
> dynamics, after three successful energy minimizations (1st: charges screened
> and no bond constraints, 2nd: charges felt but no bond constraints, 3rd:
> charges felt and bond constraints on)
> [ploetz at cluster AddRemainingVacuumBack]$ grompp -f eq4.mdp -c em3.pdb -o
> eq4.tpr -n index.ndx -p sys.top -nice 0
> :-) G R O M A C S (-:
>
> Green Red Orange Magenta Azure Cyan Skyblue
>
> :-) VERSION 4.6 (-:
>
> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2012,2013, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> This program is free software; you can redistribute it and/or
> modify it under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> :-) grompp (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -f eq4.mdp Input grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c em3.pdb Input Structure file: gro g96 pdb tpr etc.
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
> -n index.ndx Input, Opt! Index file
> -p sys.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o eq4.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file
> -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -[no]version bool no Print version info and quit
> -nice int 0 Set the nicelevel
> -[no]v bool no Be loud and noisy
> -time real -1 Take frame at or first after this time.
> -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
> sites
> -maxwarn int 0 Number of allowed warnings during input
> processing. Not for normal use and may generate
> unstable systems
> -[no]zero bool no Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum bool yes Renumber atomtypes and minimize number of
> atomtypes
>
> Ignoring obsolete mdp entry 'cpp'
> Ignoring obsolete mdp entry 'domain-decomposition'
> Ignoring obsolete mdp entry 'andersen_seed'
> Ignoring obsolete mdp entry 'nstcheckpoint'
> Replacing old mdp entry 'unconstrained-start' by 'continuation'
>
> NOTE 1 [file eq4.mdp]:
> The Berendsen thermostat does not generate the correct kinetic energy
> distribution. You might want to consider using the V-rescale thermostat.
>
> Generated 80 of the 91 non-bonded parameter combinations
> Excluding 2 bonded neighbours molecule type 'COSM'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'COSG2'
> turning all bonds into constraints...
> Velocities were taken from a Maxwell distribution at 300.15 K
> Cleaning up constraints and constant bonded interactions with virtual sites
> Number of degrees of freedom in T-Coupling group MOH is 8243.62
> Number of degrees of freedom in T-Coupling group SOL is 57717.38
> Largest charge group radii for Van der Waals: 0.118, 0.118 nm
> Largest charge group radii for Coulomb: 0.118, 0.118 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 48x48x288, spacing 0.120 0.120 0.120
> Estimate for the relative computational load of the PME mesh part: 0.37
> This run will generate roughly 622 Mb of data
>
> There was 1 note
>
> gcq#228: "Bailed Out Of Edge Synchronization After 10,000 Iterations"
> (X/Motif)
>
> [ploetz at cluster AddRemainingVacuumBack]$ more eq4.mdp
> ; VARIOUS PREPROCESSING OPTIONS
> title =
> ; Preprocessor - specify a full path if necessary.
> cpp = /lib/cpp
> include =
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
> nsteps = 500000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 500
> ; group(s) for center of mass motion removal
> comm-grps =
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 500
> nstvout = 0
> nstfout = 0
> ; Checkpointing helps you continue after crashes
> nstcheckpoint = 5000
> ; Output frequency for energies to log file and energy file
> nstlog = 500
> nstenergy = 500
> ; Output frequency and precision for xtc file
> nstxtcout = 0
> xtc-precision = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps = MOH SOL
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 10
> ; ns algorithm (simple or grid)
> ns-type = Grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc = xyz
> ; nblist cut-off
> rlist = 1.0
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r = 1
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch = 0
> rvdw = 1.5
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = No
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Seperate tables between energy group pairs
> energygrp_table =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
>
> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> implicit_solvent = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> tcoupl = berendsen
> ; Groups to couple separately
> tc-grps = MOH SOL
> ; Time constant (ps) and reference temperature (K)
> tau-t = 0.1 0.1
> ref-t = 300.15 300.15
> ; Pressure coupling
> Pcoupl = no
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p = 0.5
> compressibility = 4.5e-5
> ref-p = 1
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen-vel = yes
> gen-temp = 300.15
> gen-seed = 173529
>
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> ; Type of constraint algorithm
> constraint-algorithm = Lincs
> ; Do not constrain the start configuration
> unconstrained-start = no
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 4
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 4
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 30
> ; Convert harmonic bonds to morse potentials
> morse = no
>
> ; ENERGY GROUP EXCLUSIONS
> ; Pairs of energy groups for which all non-bonded interactions are excluded
> energygrp_excl =
>
> [ploetz at cluster AddRemainingVacuumBack]$
>
> [ploetz at cluster AddRemainingVacuumBack]$ mdrun -v -s eq4.tpr -c eq4.pdb -g
> eq4.log -o eq4.trr -nice 0
> :-) G R O M A C S (-:
>
> GRoups of Organic Molecules in ACtion for Science
>
> :-) VERSION 4.6 (-:
>
> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2012,2013, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> This program is free software; you can redistribute it and/or
> modify it under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> :-) mdrun (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s eq4.tpr Input Run input file: tpr tpb tpa
> -o eq4.trr Output Full precision trajectory: trr trj cpt
> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
> format)
> -cpi state.cpt Input, Opt. Checkpoint file
> -cpo state.cpt Output, Opt. Checkpoint file
> -c eq4.pdb Output Structure file: gro g96 pdb etc.
> -e ener.edr Output Energy file
> -g eq4.log Output Log file
> -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
> -field field.xvg Output, Opt. xvgr/xmgr file
> -table table.xvg Input, Opt. xvgr/xmgr file
> -tabletf tabletf.xvg Input, Opt. xvgr/xmgr file
> -tablep tablep.xvg Input, Opt. xvgr/xmgr file
> -tableb table.xvg Input, Opt. xvgr/xmgr file
> -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi tpi.xvg Output, Opt. xvgr/xmgr file
> -tpid tpidist.xvg Output, Opt. xvgr/xmgr file
> -ei sam.edi Input, Opt. ED sampling input
> -eo edsam.xvg Output, Opt. xvgr/xmgr file
> -j wham.gct Input, Opt. General coupling stuff
> -jo bam.gct Output, Opt. General coupling stuff
> -ffout gct.xvg Output, Opt. xvgr/xmgr file
> -devout deviatie.xvg Output, Opt. xvgr/xmgr file
> -runav runaver.xvg Output, Opt. xvgr/xmgr file
> -px pullx.xvg Output, Opt. xvgr/xmgr file
> -pf pullf.xvg Output, Opt. xvgr/xmgr file
> -ro rotation.xvg Output, Opt. xvgr/xmgr file
> -ra rotangles.log Output, Opt. Log file
> -rs rotslabs.log Output, Opt. Log file
> -rt rottorque.log Output, Opt. Log file
> -mtx nm.mtx Output, Opt. Hessian matrix
> -dn dipole.ndx Output, Opt. Index file
> -multidir rundir Input, Opt., Mult. Run directory
> -membed membed.dat Input, Opt. Generic data file
> -mp membed.top Input, Opt. Topology file
> -mn membed.ndx Input, Opt. Index file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -[no]version bool no Print version info and quit
> -nice int 0 Set the nicelevel
> -deffnm string Set the default filename for all file options
> -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
> -[no]pd bool no Use particle decompostion
> -dd vector 0 0 0 Domain decomposition grid, 0 is optimize
> -ddorder enum interleave DD node order: interleave, pp_pme or
> cartesian
> -npme int -1 Number of separate nodes to be used for PME, -1
> is guess
> -nt int 0 Total number of threads to start (0 is guess)
> -ntmpi int 0 Number of thread-MPI threads to start (0 is
> guess)
> -ntomp int 0 Number of OpenMP threads per MPI process/thread
> to start (0 is guess)
> -ntomp_pme int 0 Number of OpenMP threads per MPI process/thread
> to start (0 is -ntomp)
> -pin enum auto Fix threads (or processes) to specific cores:
> auto, on or off
> -pinoffset int 0 The starting logical core number for pinning to
> cores; used to avoid pinning threads from
> different mdrun instances to the same core
> -pinstride int 0 Pinning distance in logical cores for threads,
> use 0 to minimize the number of threads per
> physical core
> -gpu_id string List of GPU id's to use
> -[no]ddcheck bool yes Check for all bonded interactions with DD
> -rdd real 0 The maximum distance for bonded interactions
> with
> DD (nm), 0 is determine from initial coordinates
> -rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
> -dlb enum auto Dynamic load balancing (with DD): auto, no or
> yes
> -dds real 0.8 Minimum allowed dlb scaling of the DD cell size
> -gcom int -1 Global communication frequency
> -nb enum auto Calculate non-bonded interactions on: auto, cpu,
> gpu or gpu_cpu
> -[no]tunepme bool yes Optimize PME load between PP/PME nodes or
> GPU/CPU
> -[no]testverlet bool no Test the Verlet non-bonded scheme
> -[no]v bool yes Be loud and noisy
> -[no]compact bool yes Write a compact log file
> -[no]seppot bool no Write separate V and dVdl terms for each
> interaction type and node to the log file(s)
> -pforce real -1 Print all forces larger than this (kJ/mol nm)
> -[no]reprod bool no Try to avoid optimizations that affect binary
> reproducibility
> -cpt real 15 Checkpoint interval (minutes)
> -[no]cpnum bool no Keep and number checkpoint files
> -[no]append bool yes Append to previous output files when continuing
> from checkpoint instead of adding the simulation
> part number to all file names
> -nsteps int -2 Run this number of steps, overrides .mdp file
> option
> -maxh real -1 Terminate after 0.99 times this time (hours)
> -multi int 0 Do multiple simulations in parallel
> -replex int 0 Attempt replica exchange periodically with this
> period (steps)
> -nex int 0 Number of random exchanges to carry out each
> exchange interval (N^3 is one suggestion). -nex
> zero or not specified gives neighbor replica
> exchange.
> -reseed int -1 Seed for replica exchange, -1 is generate a seed
> -[no]ionize bool no Do a simulation including the effect of an X-Ray
> bombardment on your system
>
> Reading file eq4.tpr, VERSION 4.6 (single precision)
> Using 12 MPI threads
> starting mdrun 'COSM in water x_COSM 0.125'
> 500000 steps, 1000.0 ps.
> Segmentation fault
> [ploetz at cluster AddRemainingVacuumBack]$
>
> [ploetz at cluster AddRemainingVacuumBack]$ more sys.top
> #include "polff.itp"
> #include "cosm.itp"
> #include "cosg2.itp"
> [ system ]
> ; Name
> COSM in water x_COSM 0.125
> [ molecules ]
> ; Compound #mols
> COSM 1374
> COSG2 9620
>
>
> [ploetz at cluster AddRemainingVacuumBack]$ more polff.itp
>
> ;Polarizable force field atom types
> ;Includes types for COS/G2 (water) COS/M (MeOH 1-site) and CPC (MeOH 2-site)
> [ defaults ]
> LJ Geometric
> [ atomtypes ]
> ;name mass charge ptype c6 c12
> WO 15.99940 0.0 A 0.0 0.0
> WH 1.00800 0.0 A 0.0 0.0
> WD 0.00000 0.0 D 0.0 0.0
> CSMO 15.99940 0.0 A 0.0 0.0
> CSMH 1.00800 0.0 A 0.0 0.0
> CSMC 15.03500 0.0 A 0.0 0.0
> CPCO 15.99940 0.0 A 0.0 0.0
> CPCH 1.00800 0.0 A 0.0 0.0
> CPCC 15.03500 0.0 A 0.0 0.0
> WS 0.00000 0.0 S 0.0 0.0
> CSMS 0.00000 0.0 S 0.0 0.0
> CPCSC 0.00000 0.0 S 0.0 0.0
> CPCSO 0.00000 0.0 S 0.0 0.0
> [ nonbond_params ]
> ;NB: mix of COSM and CPC not included
> ;NB: includes special COSMC - COS/G2 C12 parameters
> WO WO 1 3.24434e-03 3.45765e-06
> WO CSMO 1 2.71125e-03 3.00305e-06
> WO CSMC 1 5.36612e-03 7.71936e-06
> WO CPCO 1 2.68847e-03 2.74273e-06
> WO CPCC 1 6.35721e-03 10.57112e-06
> CSMO CSMO 1 2.26576e-03 2.60823e-06
> CSMO CSMC 1 4.48440e-03 7.10600e-06
> CSMC CSMC 1 8.87552e-03 19.36000e-06
> CPCO CPCO 1 2.22784e-03 2.17563e-06
> CPCO CPCC 1 5.26799e-03 8.38538e-06
> CPCC CPCC 1 12.45679e-03 32.31923e-06
> [ploetz at cluster AddRemainingVacuumBack]$
>
> [ploetz at cluster AddRemainingVacuumBack]$ more cosm.itp
>
> ; Topology for COS/M methanol model
> ; Yu et al. J., Comput. Chem. 27 (1494-1504), 2006
> [ moleculetype ]
> ; molname nrexcl
> COSM 2
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 CSMO 1 MOH OM 1 7.470
> 2 CSMH 1 MOH HM 1 0.360
> 3 CSMC 1 MOH CM 1 0.170
> 4 CSMS 1 MOH SOM 1 -8.000
> [ polarization ]
> ;Center Shell funct alpha (nm^3)
> 1 4 1 0.001320
> [ constraints ]
> ; ai aj funct length
> 1 2 2 0.1000
> 1 3 2 0.1430
> 2 3 2 0.1988
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2 3 4
> 2 1 3 4
> 3 1 2 4
> 4 1 2 3
> #ifdef POSRES
> [ position_restraints ]
> ; iatom type fx fy fz
> 1 1 100 100 100
> 3 1 100 100 100
> #endif
> [ploetz at cluster AddRemainingVacuumBack]$
> [ploetz at cluster AddRemainingVacuumBack]$ more cosg2.itp
>
> ; Topology for COS/G2 water model
> ; Yu and Van Gunsteren, J. Chem. Phys. 121 (9549-9564), 2004
> [ moleculetype ]
> ; molname nrexcl
> COSG2 2
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 WO 1 SOL OW 1 0.0000
> 2 WH 1 SOL HW1 1 0.5265
> 3 WH 1 SOL HW2 1 0.5265
> 4 WD 1 SOL MW 1 6.9470
> 5 WS 1 SOL SW 1 -8.0000
> [ polarization ]
> ;Center Shell funct alpha (nm^3)
> 4 5 1 0.001255
> [ settles ]
> ; i funct dOH dHH
> 1 1 0.09572 0.15139
> [ dummies3 ]
> ; The position of the dummies is computed as follows:
> ;
> ; O
> ;
> ; D
> ;
> ; H H
> ;
> ; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
> ; 0.022 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ]
> ; 0.022 nm / 0.058588228 nm
> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)
> ; Dummy from funct a b
> 4 1 2 3 1 0.187751028 0.187751028
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2 3 4 5
> 2 1 3 4 5
> 3 1 2 4 5
> 4 1 2 3 5
> 5 1 2 3 4
> #ifdef POSRES
> [ position_restraints ]
> ; iatom type fx fy fz
> 1 1 100 100 100
> #endif
> [ploetz at cluster AddRemainingVacuumBack]$
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-6-4-5-3-qualitative-differences-4-6-instability-in-polarizable-force-field-vacuum-liquid-ms-tp5012174.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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