[gmx-users] problems with the output of pullx
Alfredo E. Cardenas
alfredo at ices.utexas.edu
Thu Feb 22 17:25:23 CET 2018
Hi,
I am using gromacs to get the PMF of a peptide of about 20 amino acids, moving inside of a bilayer membrane. After pulling the peptide inside the membrane now I am using pull-coord1-type = umbrella
and pull-coord1-geometry = distance to sample configurations in each window for the umbrella simulations along the z axis (axis perpendicular to the membrane surface). Runs finish ok, no error messages. The problem is that when I looked at the contents of the pullx file I observed spikes (up to 5 or more Angstroms) in the z coordinate separating the center of mass of the peptide from the membrane center. But when I extract the z coordinates of the center of mass of the two groups and compute the difference the values look reasonable with no spikes.
Here an example (it starts good):
time (ps) from pullx from traj analysis
200000.000 0.475923002 0.475919992
200010.000 0.498394012 0.498389989
200020.000 0.527589977 0.527589977
200030.000 0.491834015 0.493739992
200040.000 0.485377997 0.485379994
200050.000 0.488474995 0.488469988
200060.000 0.507991016 0.507990003
200070.000 0.475095987 0.475100011
200080.000 0.465889990 0.465889990
200090.000 0.515878975 0.515879989
200100.000 0.501435995 0.501429975
200110.000 0.505191982 0.505190015
Here a bad section:
214000.000 0.427343011 0.601450026
214010.000 0.484564990 0.545799971
214020.000 0.530139029 0.603110015
214030.000 0.176231995 0.650319993
214040.000 0.342045009 0.637109995
214050.000 0.181202993 0.636659980
214060.000 0.338808000 0.595300019
214070.000 0.442301005 0.547529995
214080.000 0.396046013 0.565050006
214090.000 0.431407988 0.538460016
214100.000 0.402586013 0.568250000
214110.000 0.438223004 0.575810015
Then good again:
230000.000 0.477869004 0.477869987
230010.000 0.511840999 0.511839986
230020.000 0.469146013 0.469150007
230030.000 0.480194002 0.480190009
230040.000 0.525618017 0.525619984
230050.000 0.498955995 0.498950005
230060.000 0.489230990 0.489230007
230070.000 0.531931996 0.531930029
230080.000 0.535376012 0.535380006
230090.000 0.488822013 0.488830000
230100.000 0.510704994 0.510699987
230110.000 0.524537981 0.524540007
230120.000 0.513199985 0.513189971
This problem happens in most umbrella windows that I have examined, sometimes several times during the long trajectories I am running. The pullf output also have those spikes.
Here is the mdp file I am using:
integrator = md
dt = 0.002
nsteps = 50000000
nstlog = 10000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstcalcenergy = 500
nstenergy = 500
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
tcoupl = Nose-Hoover
tc_grps = PROT MEMB SOL_ION
tau_t = 1.0 1.0 1.0
ref_t = 303.15 303.15 303.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 500
comm_mode = linear
comm_grps = PROT_MEMB SOL_ION
;
refcoord_scaling = com
;
pull = yes
pull-coord1-type = umbrella
pull-coord1-geometry = distance
pull-coord1-dim = N N Y
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups = 1 2
pull-group1-name = MEMB
pull-group2-name = PROT
pull-coord1-init = 0.400
pull-coord1-k = 1000 ; kJ mol^-1 nm^-2
pull-nstxout = 500 ; every 1 ps
pull-nstfout = 500 ; every 1 ps
I am not sure what is wrong here. It seems a bug to me.
Here is the header of the log file:
Log file opened on Thu Feb 15 11:09:05 2018
Host: sb202 pid: 254782 rank ID: 0 number of ranks: 112
:-) GROMACS - mdrun_mpi, 2016.4 (-:
GROMACS: mdrun_mpi, version 2016.4
Command line:
mdrun_mpi -v -cpi state8.2.cpt -deffnm constraint8.3 -cpo state8.3.cpt -noappend
GROMACS version: 2016.4
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support: disabled
SIMD instructions: AVX_256
FFT library: fftw-3.3.3-sse2
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.11.0
Tracing support: disabled
Built on: Fri Jan 26 09:28:05 MST 2018
Built by: aecarde at skybridge-login11 [CMAKE]
Build OS/arch: Linux 3.10.0-514.26.1.1chaos.ch6_1.x86_64 x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
Build CPU family: 6 Model: 45 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /opt/intel/16.0/bin/intel64/icc Intel 16.0.2.20160204
C compiler flags: -mavx -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
C++ compiler: /opt/intel/16.0/bin/intel64/icpc Intel 16.0.2.20160204
C++ compiler flags: -mavx -std=c++0x -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
Running on 7 nodes with total 112 cores, 112 logical cores
Cores per node: 16
Logical cores per node: 16
Thanks for any help
Alfredo
Alfredo E. Cardenas, PhD
Institute of Computational Engineering and Sciences (ICES)
1 University Station, C0200
University of Texas
Austin, TX 78712
Office: (512)232-5164
alfredo at ices.utexas.edu <mailto:alfredo at ices.utexas.edu>
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