how can i solve it. plz tell me !!!
GROMACS - gmx grompp, 2020.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS 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.
GROMACS: gmx grompp, version 2020.4
Executable: /data/share/tools/_conda/envs/__gromacs@2020.4/bin.AVX2_256/gmx
Data prefix: /data/share/tools/_conda/envs/__gromacs@2020.4
Working dir: /data/share/staging/26882695/working
Command line:
gmx grompp -f ./md.mdp -c ./inp.gro -r ./inp.gro -n ./index.ndx -p ./top_input.top -o outp.tpr
Ignoring obsolete mdp entry ātitleā
Ignoring obsolete mdp entry āns_typeā
Setting the LD random seed to 1778243130
Generated 3003 of the 3003 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3003 of the 3003 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type āProtein_chain_Aā
Excluding 3 bonded neighbours molecule type āUNLā
Excluding 2 bonded neighbours molecule type āSOLā
Excluding 1 bonded neighbours molecule type āNAā
Number of degrees of freedom in T-Coupling group Protein_UNL is 8356.84
Number of degrees of freedom in T-Coupling group Water_and_ions is 153369.16
Estimate for the relative computational load of the PME mesh part: 0.15
GROMACS reminds you: āWeaseling out of things is important to learn. Itās what separates us from the animalsā¦ except the weasels.ā (Homer Simpson)
turning H bonds into constraintsā¦
turning H bonds into constraintsā¦
turning H bonds into constraintsā¦
turning H bonds into constraintsā¦
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.097 nm
Set rlist, assuming 4x4 atom pair-list, to 1.224 nm, buffer size 0.024 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.156 0.156 0.156
This run will generate roughly 1934 Mb of data
GROMACS - gmx mdrun, 2020.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS 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.
GROMACS: gmx mdrun, version 2020.4
Executable: /data/share/tools/_conda/envs/__gromacs@2020.4/bin/gmx_gpu
Data prefix: /data/share/tools/_conda/envs/__gromacs@2020.4
Working dir: /data/share/staging/26882695/working
Command line:
gmx_gpu mdrun -ntmpi 1 -nb gpu -pme gpu -nt 8 -deffnm outp
Reading file outp.tpr, VERSION 2020.4 (single precision)
Changing nstlist from 20 to 100, rlist from 1.224 to 1.345
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 8 OpenMP threads
starting mdrun āProtein in waterā
25000000 steps, 50000.0 ps.
Writing final coordinates.
Core t (s) Wall t (s) (%)
Time: 359512.959 44939.133 800.0
12h28:59
(ns/day) (hour/ns)
Performance: 96.130 0.250
Thanx for Using GROMACS - Have a Nice Day
title = Protein-ligand complex MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 25000000 ; 2 * 25000000 = 50000 ps (50 ns)
dt = 0.002 ; 2 fs
; Output control
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save coordinates every 10.0 ps
; Bond parameters
continuation = yes ; continuing from NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_UNL Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = no ; continuing from NPT equilibration