[gmx-users] problems with the output of pullx
alfredo
alfredo at ices.utexas.edu
Sat Feb 24 23:43:42 CET 2018
Hi Mark,
Thanks for your comment. No, that is not the problem. At that location
the center of mass of the peptide is deep inside the membrane,
separation between the two pulling groups is 0.4 nm and the dimension of
the cell along z is more than 10 nm. I am only pulling along the z
direction. The puzzle to me is that when I extract the center of mass
separation along z between the same two groups using gmx traj those
spikes don't show up at the times when they are shown in the pullx file.
Alfredo
On 2018-02-24 11:57, Mark Abraham wrote:
> Hi,
>
> My (thoroughly uneducated) guess is that the spikes are related to the
> pull
> distance approaching half of the dimensions of the cell. Not all
> flavours
> of pulling can handle this. Might that be the issue?
>
> Mark
>
> On Sat, Feb 24, 2018, 17:55 alfredo <alfredo at ices.utexas.edu> wrote:
>
>> Hi,
>> Updating my post. The problem has been observed in two different
>> machine
>> systems (the latest I have found the problem was the skylake nodes in
>> tacc). I assumed it has to be some communication bug of coordinates
>> and
>> forces in the pull part of the code. Probably observed in my case
>> because of the large size of the peptide I am pulling inside the
>> membrane. For now I am thinking to extract coordinates from the trr
>> file
>> and from them compute the pulling harmonic forces. But not an ideal
>> solution.
>> Thanks
>> Alfredo
>>
>>
>>
>>
>> On 2018-02-22 10:17, Alfredo E. Cardenas wrote:
>> > 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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