[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule
Sandipan Dutta
sandy0207 at gmail.com
Thu Feb 20 04:27:30 CET 2014
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.
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.
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> 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 | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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