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@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
alfr...@ices.utexas.edu <mailto:alfr...@ices.utexas.edu>



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