[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule
Justin Lemkul
jalemkul at vt.edu
Thu Feb 20 04:33:00 CET 2014
On 2/19/14, 10:27 PM, Sandipan Dutta wrote:
> Dear GMX users:
>
> Thanks a lot for the reply Justin. I have put a bond between OW and DOH2 and
> have set nrexcl to 2 in the .itp file . The grompp command now produces a note:
>
> NOTE 1 [file grompp1.mdp]:
> The optimal PME mesh load for parallel simulations is below 0.5
> and for highly parallel simulations between 0.25 and 0.33,
> for higher performance, increase the cut-off and the PME grid spacing.
>
> When I run the mdrun the simulation stops at step 0 and I get a Segmentation
> fault error. I am getting nan for the (SR) Coulomb energy in the log file. I
> was suspecting the
> Coulomb potential between OW and DOH2 is causing the nan error because the bond
> length is 0. But nrexcl to 2 removes the problem I guess.
>
Right, there are no intramolecular nonbonded interactions here.
> Can someone please point me in the right direction? I have attached the .mdp
> file and the log file below. I am getting the same errors when I simulated 1
> swm4 molecule instead of 216 molecules.
>
The topology is more relevant.
Does energy minimization work? Are you simulating only a single molecule?
Based on the energies in the .log, that seems to be the only explanation.
-Justin
> Thanks a lot.
>
> Sandipan Dutta
> APCTP, South Korea
>
> .mdp file
> ----------------------------------------------------------------------------------------------------------------------------------------
> -----------------------------------------------------------------------------------------------------------------------------------------
> integrator = md
>
> dt = 0.0001 ; time step
>
> nsteps = 1000000 ; number of steps
>
> comm_mode = Linear;Angular ; Remove center of mass
> translation and rotation
>
> nstcomm = 1003 ; reset c.o.m. motion
>
> nstxout = 10000 ; write coords
>
> nstvout = 10000 ; write velocities
>
> nstxtcout = 2000 ; write coords to xtc-trajectory file
>
> nstlog = 2000 ; print to logfile
>
> nstlist = 20 ; update pairlist
>
> ns_type = grid ;simple ; pairlist method
>
> ;================== Polarizable model parameters =======================
>
> emtol = 0.1 ;the convergency criterion for maximum force
>
> niter = 20 ;maximum number of iterations for the
> shell particle optimization
>
> ;================= Cutt off specification =============================
>
> pbc = xyz ; periodic boundary conditions
>
> optimize_fft = yes ; perform FFT optimization at start
>
> coulombtype = PME
>
> rcoulomb = 1.5 ; cut-off for coulomb
>
> rlist = 1.5 ; cut-off for ns
>
> vdw-type = cut-off
>
> rvdw = 1.5 ; cut-off for vdw
>
> dispcorr = enerpres
>
> ;=======================================================================
>
> Tcoupl = v-rescale ; berendsen;nose-hoover; ; ;
> temperature coupling
>
> tc-grps = SWM4
>
> ref_t = 298.15
>
> tau_t = 0.1
>
> Pcoupl = berendsen ; pressure bath
>
> Pcoupltype = isotropic ; pressure geometry
>
> tau_p = 0.5 ; p-coupoling time
>
> compressibility = 4.5e-5 ;
>
> ref_p = 1.01325
>
> ;=======================================================================
>
> gen_vel = no ; generate initial velocities
>
> gen_temp = 300 ; initial temperature
>
> gen_seed = 1903 ; random seed
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>
> .log file
> ___________________________________________________________________________________________
> ______________________________________________________________________________________
>
> Log file opened on Thu Feb 20 12:02:47 2014
> Host: sandip0207-HP-Compaq-6200-Pro-MT-PC pid: 32505 nodeid: 0 nnodes: 1
> Gromacs version: VERSION 4.6.3
> Precision: single
> Memory model: 64 bit
> MPI library: thread_mpi
> OpenMP support: enabled
> GPU support: disabled
> invsqrt routine: gmx_software_invsqrt(x)
> CPU acceleration: AVX_256
> FFT library: fftw-3.3.2-sse2
> Large file support: enabled
> RDTSCP usage: enabled
> Built on: 2013. 07. 23. (화) 21:00:03 KST
> Built by: sandip0207 at sandip0207-HP-Compaq-6200-Pro-MT-PC [CMAKE]
> Build OS/arch: Linux 3.8.0-26-generic x86_64
> Build CPU vendor: GenuineIntel
> Build CPU brand: Intel(R) Core(TM) i5-2500 CPU @ 3.30GHz
> Build CPU family: 6 Model: 42 Stepping: 7
> Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
> tdt x2apic
> C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
> C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
>
>
> :-) G R O M A C S (-:
>
> S C A M O R G
>
> :-) VERSION 4.6.3 (-:
>
> 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 (-:
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
> molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 435-447
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
> Berendsen
> GROMACS: Fast, Flexible and Free
> J. Comp. Chem. 26 (2005) pp. 1701-1719
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> E. Lindahl and B. Hess and D. van der Spoel
> GROMACS 3.0: A package for molecular simulation and trajectory analysis
> J. Mol. Mod. 7 (2001) pp. 306-317
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
> GROMACS: A message-passing parallel molecular dynamics implementation
> Comp. Phys. Comm. 91 (1995) pp. 43-56
> -------- -------- --- Thank You --- -------- --------
>
> Input Parameters:
> integrator = md
> nsteps = 1000000
> init-step = 0
> cutoff-scheme = Group
> ns_type = Grid
> nstlist = 20
> ndelta = 2
> nstcomm = 1003
> comm-mode = Linear
> nstlog = 2000
> nstxout = 10000
> nstvout = 10000
> nstfout = 0
> nstcalcenergy = 100
> nstenergy = 1000
> nstxtcout = 2000
> init-t = 0
> delta-t = 0.0001
> xtcprec = 1000
> fourierspacing = 0.12
> nkx = 42
> nky = 44
> nkz = 44
> pme-order = 4
> ewald-rtol = 1e-05
> ewald-geometry = 0
> epsilon-surface = 0
> optimize-fft = TRUE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = V-rescale
> bPrintNHChains = FALSE
> nsttcouple = 20
> epc = Berendsen
> epctype = Isotropic
> nstpcouple = 20
> tau-p = 0.5
> ref-p (3x3):
> ref-p[ 0]={ 1.01325e+00, 0.00000e+00, 0.00000e+00}
> ref-p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00}
> ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+00}
> compress (3x3):
> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
> refcoord-scaling = No
> posres-com (3):
> posres-com[0]= 0.00000e+00
> posres-com[1]= 0.00000e+00
> posres-com[2]= 0.00000e+00
> posres-comB (3):
> posres-comB[0]= 0.00000e+00
> posres-comB[1]= 0.00000e+00
> posres-comB[2]= 0.00000e+00
> verlet-buffer-drift = 0.005
> rlist = 1.5
> rlistlong = 1.5
> nstcalclr = 0
> rtpi = 0.05
> coulombtype = PME
> coulomb-modifier = None
> rcoulomb-switch = 0
> rcoulomb = 1.5
> vdwtype = Cut-off
> vdw-modifier = None
> rvdw-switch = 0
> rvdw = 1.5
> epsilon-r = 1
> epsilon-rf = inf
> tabext = 1
> implicit-solvent = No
> gb-algorithm = Still
> gb-epsilon-solvent = 80
> nstgbradii = 1
> rgbradii = 1
> gb-saltconc = 0
> gb-obc-alpha = 1
> gb-obc-beta = 0.8
> gb-obc-gamma = 4.85
> gb-dielectric-offset = 0.009
> sa-algorithm = Ace-approximation
> sa-surface-tension = 2.05016
> DispCorr = EnerPres
> bSimTemp = FALSE
> free-energy = no
> nwall = 0
> wall-type = 9-3
> wall-atomtype[0] = -1
> wall-atomtype[1] = -1
> wall-density[0] = 0
> wall-density[1] = 0
> wall-ewald-zfac = 3
> pull = no
> rotation = FALSE
> disre = No
> disre-weighting = Conservative
> disre-mixed = FALSE
> dr-fc = 1000
> dr-tau = 0
> nstdisreout = 100
> orires-fc = 0
> orires-tau = 0
> nstorireout = 100
> dihre-fc = 0
> em-stepsize = 0.01
> em-tol = 0.1
> niter = 20
> fc-stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake-tol = 0.0001
> lincs-order = 4
> lincs-warnangle = 30
> lincs-iter = 1
> bd-fric = 0
> ld-seed = 1993
> cos-accel = 0
> deform (3x3):
> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> adress = FALSE
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 6
> ref-t: 298.15
> tau-t: 0.1
> anneal: No
> ann-npoints: 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp-flags[ 0]: 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm-opts:
> ngQM = 0
> Using 1 MPI thread
>
> Detecting CPU-specific acceleration.
> Present hardware specification:
> Vendor: GenuineIntel
> Brand: Intel(R) Core(TM) i5-2500 CPU @ 3.30GHz
> Family: 6 Model: 42 Stepping: 7
> Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid
> pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> Acceleration most likely to fit this hardware: AVX_256
> Acceleration selected at GROMACS compile time: AVX_256
>
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw: FALSE
> Will do PME sum in reciprocal space.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
>
> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.480244 nm for Ewald
> Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.5
> Long Range LJ corr.: <C6> 0.0000e+00
> System total charge: 0.000
> Generated table with 1250 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1250 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1250 data points for LJ12.
> Tabscale = 500 points/nm
> Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00
> Initialized non-bonded Ewald correction tables, spacing: 8.08e-04 size: 3095
>
> Removing pbc first time
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> G. Bussi, D. Donadio and M. Parrinello
> Canonical sampling through velocity rescaling
> J. Chem. Phys. 126 (2007) pp. 014101
> -------- -------- --- Thank You --- -------- --------
>
> There are: 3 Atoms
> There are: 2 VSites
> Max number of connections per atom is 4
> Total number of connections is 8
> Max number of graph edges per atom is 2
> Total number of graph edges is 4
> Initial temperature: 0 K
>
> Started mdrun on node 0 Thu Feb 20 12:02:47 2014
>
> Step Time Lambda
> 0 0.00000 0.00000
>
>
> Grid: 3 x 3 x 3 cells
> Energies (kJ/mol)
> Bond Angle LJ (SR) Disper. corr. Coulomb (SR)
> 1.25581e-01 2.90704e-02 0.00000e+00 0.00000e+00 -nan
> Coul. recip. Potential Kinetic En. Total Energy Temperature
> -1.95174e+03 -nan -nan -nan -nan
> Pres. DC (bar) Pressure (bar)
> 0.00000e+00 -nan
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________________________________________________________
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Wed, Feb 12, 2014 at 11:19 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 2/12/14, 12:52 AM, Sandipan Dutta wrote:
>
> Dear GMX users:
>
> I am fairly new to gromacs. I am trying to simulate SWM4 water model. In
> the model the electrostatic interactions between the Drude particle (DOH2)
> and oxygen atom (OP) are excluded. I have created an index file index.ndx
> that contains the numbers of the DOH2 and OP atoms. In the grompp.mdp file
> I have used the energygrp_excl command to exclude the energies between the
> groups. But when I run the grompp command:
>
> grompp -maxwarn 3 -n index.ndx
>
> I get the following error:
>
> WARNING 1 [file grompp.mdp]:
> Can not exclude the lattice Coulomb energy between energy groups
>
> Fatal error:
> atoms 1 and 2 in charge group 1 of molecule type 'Other' are in different
> energy groups
>
> I have attached the grompp.mdp and the index.ndx files. Can someone please
> help me with these?
>
>
> The attachments didn't survive.
>
> Why do you need special index groups for doing this? The Drude models
> should have a bond between DOH2 and OH2, and setting nrexcl to 2 will
> exclude these interactions.
>
> -Justin
>
> --
> ==============================__====================
>
> Justin A. Lemkul, Ph.D.
> 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
> <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> <tel:%28410%29%20706-7441>
> http://mackerell.umaryland.__edu/~jalemkul
> <http://mackerell.umaryland.edu/~jalemkul>
>
> ==============================__====================
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--
==================================================
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
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