Re: [gmx-users] OPLS parameters for O2
Den 2019-05-10 kl. 00:42, skrev Shadi Fuladi: Hi, I'm trying to test molecular oxygen diffusion in electrolytes using OPLS force field. Is there any O2 parameters tested with OPLS AA forcefield? Thanks, SF There is a model described here Hub, J. S.; de Groot, B. L. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1198−1203. that we have tested in the paper below and it has has quite accurate solubility in water. See Michiel van Lun, Jochen S. Hub, David van der Spoel and Inger Andersson: CO2 and O2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir J. Amer. Chem. Soc. 136 pp. 3165-3171 (2014) Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)
Yup, your assessment agrees with our guess. Our HPC guru will be taking his findings, along with your quote, to the admins. Thank you, Alex On Thu, May 9, 2019 at 2:51 PM Szilárd Páll wrote: > On Thu, May 9, 2019 at 10:01 PM Alex wrote: > > > Okay, we're positively unable to run a Gromacs (2019.1) test on Power9. > The > > test procedure is simple, using slurm: > > 1. Request an interactive session: > srun -N 1 -n 20 --pty > > --partition=debug --time=1:00:00 --gres=gpu:1 bash > > 2. Load CUDA library: module load cuda > > 3. Run test batch. This starts with a CPU-only static EM, which, despite > > the mdrun variables, runs on a single thread. Any help will be highly > > appreciated. > > > > md.log below: > > > > GROMACS: gmx mdrun, version 2019.1 > > Executable: /home/reida/ppc64le/stow/gromacs/bin/gmx > > Data prefix: /home/reida/ppc64le/stow/gromacs > > Working dir: /home/smolyan/gmx_test1 > > Process ID: 115831 > > Command line: > > gmx mdrun -pin on -pinstride 2 -ntomp 4 -ntmpi 4 -pme cpu -nb cpu -s > > em.tpr -o traj.trr -g md.log -c after_em.pdb > > > > GROMACS version:2019.1 > > Precision: single > > Memory model: 64 bit > > MPI library:thread_mpi > > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > > GPU support:CUDA > > SIMD instructions: IBM_VSX > > FFT library:fftw-3.3.8 > > RDTSCP usage: disabled > > TNG support:enabled > > Hwloc support: hwloc-1.11.8 > > Tracing support:disabled > > C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc GNU 7.3.1 > > C compiler flags: -mcpu=power9 -mtune=power9 -mvsx -O2 -DNDEBUG > > -funroll-all-loops -fexcess-precision=fast > > C++ compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ GNU 7.3.1 > > C++ compiler flags: -mcpu=power9 -mtune=power9 -mvsx-std=c++11 -O2 > > -DNDEBUG -funroll-all-loops -fexcess-precision=fast > > CUDA compiler: /usr/local/cuda-10.0/bin/nvcc nvcc: NVIDIA (R) Cuda > > compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on > > Sat_Aug_25_21:10:00_CDT_2018;Cuda compilation tools, release 10.0, > > V10.0.130 > > CUDA compiler > > > > > flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;; > > > > > -mcpu=power9;-mtune=power9;-mvsx;-std=c++11;-O2;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; > > CUDA driver:10.10 > > CUDA runtime: 10.0 > > > > > > Running on 1 node with total 160 cores, 160 logical cores, 1 compatible > GPU > > Hardware detected: > > CPU info: > > Vendor: IBM > > Brand: POWER9, altivec supported > > Family: 0 Model: 0 Stepping: 0 > > Features: vmx vsx > > Hardware topology: Only logical processor count > > GPU info: > > Number of GPUs detected: 1 > > #0: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: > > compatible > > > > > > PLEASE READ AND CITE THE FOLLOWING REFERENCE > > > > *SKIPPED* > > > > Input Parameters: > >integrator = steep > >tinit = 0 > >dt = 0.001 > >nsteps = 5 > >init-step = 0 > >simulation-part= 1 > >comm-mode = Linear > >nstcomm= 100 > >bd-fric= 0 > >ld-seed= 1941752878 > >emtol = 100 > >emstep = 0.01 > >niter = 20 > >fcstep = 0 > >nstcgsteep = 1000 > >nbfgscorr = 10 > >rtpi = 0.05 > >nstxout= 0 > >nstvout= 0 > >nstfout= 0 > >nstlog = 1000 > >nstcalcenergy = 100 > >nstenergy = 1000 > >nstxout-compressed = 0 > >compressed-x-precision = 1000 > >cutoff-scheme = Verlet > >nstlist= 1 > >ns-type= Grid > >pbc= xyz > >periodic-molecules = true > >verlet-buffer-tolerance= 0.005 > >rlist = 1.2 > >coulombtype= PME > >coulomb-modifier = Potential-shift > >rcoulomb-switch= 0 > >rcoulomb = 1.2 > >epsilon-r = 1 > >epsilon-rf = inf > >vdw-type = Cut-off
[gmx-users] OPLS parameters for O2
Hi, I'm trying to test molecular oxygen diffusion in electrolytes using OPLS force field. Is there any O2 parameters tested with OPLS AA forcefield? Thanks, SF -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)
On Thu, May 9, 2019 at 10:01 PM Alex wrote: > Okay, we're positively unable to run a Gromacs (2019.1) test on Power9. The > test procedure is simple, using slurm: > 1. Request an interactive session: > srun -N 1 -n 20 --pty > --partition=debug --time=1:00:00 --gres=gpu:1 bash > 2. Load CUDA library: module load cuda > 3. Run test batch. This starts with a CPU-only static EM, which, despite > the mdrun variables, runs on a single thread. Any help will be highly > appreciated. > > md.log below: > > GROMACS: gmx mdrun, version 2019.1 > Executable: /home/reida/ppc64le/stow/gromacs/bin/gmx > Data prefix: /home/reida/ppc64le/stow/gromacs > Working dir: /home/smolyan/gmx_test1 > Process ID: 115831 > Command line: > gmx mdrun -pin on -pinstride 2 -ntomp 4 -ntmpi 4 -pme cpu -nb cpu -s > em.tpr -o traj.trr -g md.log -c after_em.pdb > > GROMACS version:2019.1 > Precision: single > Memory model: 64 bit > MPI library:thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > GPU support:CUDA > SIMD instructions: IBM_VSX > FFT library:fftw-3.3.8 > RDTSCP usage: disabled > TNG support:enabled > Hwloc support: hwloc-1.11.8 > Tracing support:disabled > C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc GNU 7.3.1 > C compiler flags: -mcpu=power9 -mtune=power9 -mvsx -O2 -DNDEBUG > -funroll-all-loops -fexcess-precision=fast > C++ compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ GNU 7.3.1 > C++ compiler flags: -mcpu=power9 -mtune=power9 -mvsx-std=c++11 -O2 > -DNDEBUG -funroll-all-loops -fexcess-precision=fast > CUDA compiler: /usr/local/cuda-10.0/bin/nvcc nvcc: NVIDIA (R) Cuda > compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on > Sat_Aug_25_21:10:00_CDT_2018;Cuda compilation tools, release 10.0, > V10.0.130 > CUDA compiler > > flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;; > > -mcpu=power9;-mtune=power9;-mvsx;-std=c++11;-O2;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; > CUDA driver:10.10 > CUDA runtime: 10.0 > > > Running on 1 node with total 160 cores, 160 logical cores, 1 compatible GPU > Hardware detected: > CPU info: > Vendor: IBM > Brand: POWER9, altivec supported > Family: 0 Model: 0 Stepping: 0 > Features: vmx vsx > Hardware topology: Only logical processor count > GPU info: > Number of GPUs detected: 1 > #0: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: > compatible > > > PLEASE READ AND CITE THE FOLLOWING REFERENCE > > *SKIPPED* > > Input Parameters: >integrator = steep >tinit = 0 >dt = 0.001 >nsteps = 5 >init-step = 0 >simulation-part= 1 >comm-mode = Linear >nstcomm= 100 >bd-fric= 0 >ld-seed= 1941752878 >emtol = 100 >emstep = 0.01 >niter = 20 >fcstep = 0 >nstcgsteep = 1000 >nbfgscorr = 10 >rtpi = 0.05 >nstxout= 0 >nstvout= 0 >nstfout= 0 >nstlog = 1000 >nstcalcenergy = 100 >nstenergy = 1000 >nstxout-compressed = 0 >compressed-x-precision = 1000 >cutoff-scheme = Verlet >nstlist= 1 >ns-type= Grid >pbc= xyz >periodic-molecules = true >verlet-buffer-tolerance= 0.005 >rlist = 1.2 >coulombtype= PME >coulomb-modifier = Potential-shift >rcoulomb-switch= 0 >rcoulomb = 1.2 >epsilon-r = 1 >epsilon-rf = inf >vdw-type = Cut-off >vdw-modifier = Potential-shift >rvdw-switch= 0 >rvdw = 1.2 >DispCorr = No >table-extension= 1 >fourierspacing = 0.12 >fourier-nx = 52 >fourier-ny = 52 >fourier-nz = 52 >pme-order = 4 >
Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)
Okay, we're positively unable to run a Gromacs (2019.1) test on Power9. The test procedure is simple, using slurm: 1. Request an interactive session: > srun -N 1 -n 20 --pty --partition=debug --time=1:00:00 --gres=gpu:1 bash 2. Load CUDA library: module load cuda 3. Run test batch. This starts with a CPU-only static EM, which, despite the mdrun variables, runs on a single thread. Any help will be highly appreciated. md.log below: GROMACS: gmx mdrun, version 2019.1 Executable: /home/reida/ppc64le/stow/gromacs/bin/gmx Data prefix: /home/reida/ppc64le/stow/gromacs Working dir: /home/smolyan/gmx_test1 Process ID: 115831 Command line: gmx mdrun -pin on -pinstride 2 -ntomp 4 -ntmpi 4 -pme cpu -nb cpu -s em.tpr -o traj.trr -g md.log -c after_em.pdb GROMACS version:2019.1 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:CUDA SIMD instructions: IBM_VSX FFT library:fftw-3.3.8 RDTSCP usage: disabled TNG support:enabled Hwloc support: hwloc-1.11.8 Tracing support:disabled C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc GNU 7.3.1 C compiler flags: -mcpu=power9 -mtune=power9 -mvsx -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ GNU 7.3.1 C++ compiler flags: -mcpu=power9 -mtune=power9 -mvsx-std=c++11 -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda-10.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Sat_Aug_25_21:10:00_CDT_2018;Cuda compilation tools, release 10.0, V10.0.130 CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;; -mcpu=power9;-mtune=power9;-mvsx;-std=c++11;-O2;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver:10.10 CUDA runtime: 10.0 Running on 1 node with total 160 cores, 160 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: IBM Brand: POWER9, altivec supported Family: 0 Model: 0 Stepping: 0 Features: vmx vsx Hardware topology: Only logical processor count GPU info: Number of GPUs detected: 1 #0: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: compatible PLEASE READ AND CITE THE FOLLOWING REFERENCE *SKIPPED* Input Parameters: integrator = steep tinit = 0 dt = 0.001 nsteps = 5 init-step = 0 simulation-part= 1 comm-mode = Linear nstcomm= 100 bd-fric= 0 ld-seed= 1941752878 emtol = 100 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout= 0 nstvout= 0 nstfout= 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist= 1 ns-type= Grid pbc= xyz periodic-molecules = true verlet-buffer-tolerance= 0.005 rlist = 1.2 coulombtype= PME coulomb-modifier = Potential-shift rcoulomb-switch= 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch= 0 rvdw = 1.2 DispCorr = No table-extension= 1 fourierspacing = 0.12 fourier-nx = 52 fourier-ny = 52 fourier-nz = 52 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface= 0 tcoupl = No nsttcouple
[gmx-users] charge density of multiple frames in a limited region
Dear Users, In using: gmx density -f lipid.nvt.trr -s octanoate.nvt3.tpr -dens charge -center -symm -sl 100 -b 4 -e 4.5 it appears that the average charge density of all frames and the total box size is used in the calculation. Is there a way to 1) specify multiple ranges to output say, every , 20th frame other than running the command multiple times and 2) specify at least one of the x and y dimensions in which the charge density is calculated ? Regards pb -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun log file question
hello all,I am running an md simulation using gromacs 2019 with RDC restraints added in all steps, now in my log file i get something like this Orientation experiment 1: order parameter: -0.00156791 eig: 1.000 -0.085 0.037 0.996 eig: -0.636 -0.144 0.988 -0.049 eig: -0.364 0.986 0.148 0.079 Orientation experiment 2: order parameter: 0.00196219 eig: 1.000 0.497 0.569 0.655 eig: -0.596 0.785 0.027 -0.619 eig: -0.404 0.370 -0.822 0.434 so my question is what does the order parameter her represents, is it a scalling factor for the eigen values or something elsecan someone help me with thisThank youHanin OMar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] TIP4P molecules stuck together
Dr. Shirts,
Thank you for the swift reply.
> If you have "unprotected" electrostatic sites (i.e. with nonzero repulsive
> terms directly on top of the charge), then there will always be some
> configurations with essentially infinitely negative energy.
That makes sense. Definitely something to think about, especially in these
simulations.
>Is your cap smoothly varying? If not, then your dynamics on hitting the
cap will be unphysical.
Indeed, our cap is implemented instantaneously and certainly introduces
non-physical dynamics when it is triggered. Our simulations consist of
non-interacting "tracer" particles that abruptly change resolution to
fully atomistic, interacting water molecules when they pass an interface
in the simulation box.
The force cap is a brute-force approach to ensure the simulation doesn't
explode when a particle crosses the boundary, gains atomistic features,
and finds itself in an unphysical configuration relative to an already
atomistically-resolved molecule (other groups have used a Monte Carlo move
to adjust the overlapping molecules... something we may consider in the
future).
We do not consider structural/dynamic properties within this interface
region where the force-cap is triggered by the immense energies due to
particle-particle overlap.
>How are the forces propagated into the energies (if grad U
>=/= F, then weird non-newtonian physics will also happen).
The forces are normalized to 2000 (iff > 2000) just before the velocities
are calculated in the first step of the stochastic dynamics integrator.
> What are the energies? Are they lower or higher than zero?
>From the single-point energy calculation of the dimer configuration, the
potential energy output is:
Energy Average Err.Est. RMSD Tot-Drift
---
Potential503436 -- 0 0
(kJ/mol)
and the output from gmx dump:
traj.trr frame 0:
natoms=10 step= 0 time=7.144e+03 lambda= 0
box (3x3):
box[0]={ 3.36795e+01, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 7.54019e+00, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 7.54019e+00}
x (10x3):
x[0]={ 2.10910e+01, 3.64700e+00, 2.75200e+00}
x[1]={ 2.11150e+01, 3.6e+00, 2.83200e+00}
x[2]={ 2.11700e+01, 3.69400e+00, 2.72700e+00}
x[3]={ 2.11040e+01, 3.64700e+00, 2.75900e+00}
x[4]={ 2.10960e+01, 3.64700e+00, 2.75500e+00}
x[5]={ 2.11700e+01, 3.72600e+00, 2.72800e+00}
x[6]={ 2.11700e+01, 3.65300e+00, 2.66500e+00}
x[7]={ 2.10770e+01, 3.73900e+00, 2.74900e+00}
x[8]={ 2.11580e+01, 3.71800e+00, 2.72200e+00}
x[9]={ 2.11650e+01, 3.72300e+00, 2.72500e+00}
v (10x3):
v[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[3]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[4]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[5]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[6]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[7]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[8]={ 0.0e+00, 0.0e+00, 0.0e+00}
v[9]={ 0.0e+00, 0.0e+00, 0.0e+00}
f (10x3):
f[0]={-3.67300e+07, -3.67266e+07, 1.11572e+07}
f[1]={-3.54829e+02, -4.32763e+01, 3.86598e+00}
f[2]={-4.24006e+04, 9.05089e+04, -1.34170e+04}
f[3]={ 0.0e+00, 0.0e+00, 0.0e+00}
f[4]={ 0.0e+00, 0.0e+00, 0.0e+00}
f[5]={ 3.67632e+07, 3.66652e+07, -1.11462e+07}
f[6]={ 3.81472e+03, -1.38062e+04, -2.40026e+02}
f[7]={ 5.73042e+03, -1.52270e+04, 2.66433e+03}
f[8]={ 0.0e+00, 0.0e+00, 0.0e+00}
f[9]={ 0.0e+00, 0.0e+00, 0.0e+00}
note: there are 5 atoms per TIP4P molecule in our case because we use a
virtual site constructed from the other atoms as the non-interacting
"tracer" particle (all 5 atoms exist at once as a hybrid molecule all the
time, interactions are just switched on for OW, HW1, HW2, and MW when they
transition to the atomistically-resolved region)
Sorry for the wall of text, I hope what I said makes sense. I appreciate
the help.
John
> On Thu, May 9, 2019 at 8:43 AM John Whittaker <
> johnwhitt...@zedat.fu-berlin.de> wrote:
>
>> Hi all,
>>
>> I have a rather strange question that I hope someone can shed some light
>> on.
>>
>> Before I begin, I want to note that I am pioneering some new
>> developments
>> of the Adaptive Resolution Simulation technique
>> (https://doi.org/10.1002/adts.201900014), so the simulations/techniques
>> I
>> am performing/implementing are fairly non-standard with respect to
>> normal
>> atomistic
Re: [gmx-users] TIP4P molecules stuck together
If you have "unprotected" electrostatic sites (i.e. with nonzero repulsive terms directly on top of the charge), then there will always be some configurations with essentially infinitely negative energy. For vanilla MD, these are essentially impossible to reach kinetically at any reasonable temperature or reasonable timestep, because the R^-12 of the neighboring atoms creates such an enormously large barrier. But with certain accelerated sampling approaches, you can skip over the barrier, and access these sites, which will either blow up the simulation, or get stuck forever. If you cap the forces, then weirder things will happen. Is your cap smoothly varying? If not, then your dynamics on hitting the cap will be unphysical. How are the forces propagated into the energies (if grad U =/= F, then weird non-newtonian physics will also happen). > the forces on each atom are massive (on the order of 10^7). What are the energies? Are they lower or higher than zero? On Thu, May 9, 2019 at 8:43 AM John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > Hi all, > > I have a rather strange question that I hope someone can shed some light > on. > > Before I begin, I want to note that I am pioneering some new developments > of the Adaptive Resolution Simulation technique > (https://doi.org/10.1002/adts.201900014), so the simulations/techniques I > am performing/implementing are fairly non-standard with respect to normal > atomistic simulations. > > With that in mind, I am simulating a box of TIP4P water and calculating > structural/static properties. My simulations utilize a force-cap of 2000 > kJ/(mol nm) at each time step - i.e., when the force on an atom is larger > than +/- 2000, the force is automatically normalized to +/- 2000 to > prevent explosive forces due to atomic overlaps. > > For the most part, this works for the purposes of my simulations but I > have observed some water molecules "sticking" together in the > configuration shown here: > > https://www.dropbox.com/s/p5rkximspp25flf/tip4pDimer.jpg?dl=0 > > with a corresponding O-H radial distribution function (unnormalized) shown > here: > > https://www.dropbox.com/s/ez56db4qggv1iii/rdf_OH_long.jpg?dl=0 > > where there is a clear (albeit, small) probability of finding a hydrogen > atom an extremely short distance from an oxygen. > > The molecules travel together like this for several ps and then, for > seemingly no reason, split apart and carry on perfectly fine for the rest > of the simulation. > > I have performed a single-point energy calculation on this configuration > in vacuum and have found, as one would expect, the forces on each atom are > massive (on the order of 10^7). Yet, the molecules do not repel and seem > to prefer this configuration for a short time. > > I have a feeling that this configuration is allowed when the forces are > normalized to 2000 and the molecules become trapped there. > > I am wondering if anyone may have some experience with TIP4P water > molecules taking on unphysical configurations for non-negligible times. I > have not tried this same simulation using TIP3P yet, so I'm unsure if it > has something to do with electrostatic interactions with the virtual site, > but I will test this tomorrow. > > Thank you for any information/speculation/guesses as to why this is > happening. > > - John > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] TIP4P molecules stuck together
Hi all, I have a rather strange question that I hope someone can shed some light on. Before I begin, I want to note that I am pioneering some new developments of the Adaptive Resolution Simulation technique (https://doi.org/10.1002/adts.201900014), so the simulations/techniques I am performing/implementing are fairly non-standard with respect to normal atomistic simulations. With that in mind, I am simulating a box of TIP4P water and calculating structural/static properties. My simulations utilize a force-cap of 2000 kJ/(mol nm) at each time step - i.e., when the force on an atom is larger than +/- 2000, the force is automatically normalized to +/- 2000 to prevent explosive forces due to atomic overlaps. For the most part, this works for the purposes of my simulations but I have observed some water molecules "sticking" together in the configuration shown here: https://www.dropbox.com/s/p5rkximspp25flf/tip4pDimer.jpg?dl=0 with a corresponding O-H radial distribution function (unnormalized) shown here: https://www.dropbox.com/s/ez56db4qggv1iii/rdf_OH_long.jpg?dl=0 where there is a clear (albeit, small) probability of finding a hydrogen atom an extremely short distance from an oxygen. The molecules travel together like this for several ps and then, for seemingly no reason, split apart and carry on perfectly fine for the rest of the simulation. I have performed a single-point energy calculation on this configuration in vacuum and have found, as one would expect, the forces on each atom are massive (on the order of 10^7). Yet, the molecules do not repel and seem to prefer this configuration for a short time. I have a feeling that this configuration is allowed when the forces are normalized to 2000 and the molecules become trapped there. I am wondering if anyone may have some experience with TIP4P water molecules taking on unphysical configurations for non-negligible times. I have not tried this same simulation using TIP3P yet, so I'm unsure if it has something to do with electrostatic interactions with the virtual site, but I will test this tomorrow. Thank you for any information/speculation/guesses as to why this is happening. - John -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] dipole moment of water using TIP3P model
Dear Users, It is known that electric dipole moment of a water monomer is experimentally 1.85 D and using the TIP3P model it's supposed to be 2.35D. I am using the TIP3P model for a water-based simulation in Gromacs 5.1.5. After applying sinusoidal electric fields in the Y axis, the norm of the dipole vector per water molecule using *gmx dipoles* is closer to 1.85 D and nowhere near 2.35D. My simulations are for 300K and 1 atm. Can anyone guess why the discrepancy? Is it because 2.35D is for a water monomer and my system has quite a large number of them(in the order of ten thousands)? But literature suggests that presence of water molecules should enhance the dipole moment. Or is 2.35D calculated under a different temperature/pressure conditions? If you could suggest me suitable references that might clarify this issue, please let me know. Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand in water
This will do it (if need particular water model change with cs switch options, and assumes ligand.gro has the correct final box size) gmx solvate - cp ligand.gro -cs -o complex.gro Unless you have a particular number of waters required, then use.: gmx solvate - cp ligand.gro -cs -o complex.gro -maxsol To both above add -p topol.top if want it to automatically update the topology file with number of molecules/residues. Otherwise you need to do by hand, which is easy enough. Or even if need a particular water coordinate file: gmx insert-molecules -f ligand.gro -ci water.gro -nmol -o complex.gro On Thu, 9 May 2019, 7:02 pm RAHUL SURESH, wrote: > Hi Users. > > I want to simulate ligand in the water box. I prepared a water molecule and > started with pdb2gmx and then planned to follow protein-ligand tutorial. > Unfortunately ended up with an error in gro file format. Have check every > possibility but still couldn't find any solution. > My initial pdb is water.pdb and the corresponding gro file is water.gro. I > clubbed the ligand gro file and water gro file as complex.gro. I have > uploaded the file here. can anyone help me with the format issues>? > > -- > *Regards,* > *Rahul * > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ligand in water
Hi Users. I want to simulate ligand in the water box. I prepared a water molecule and started with pdb2gmx and then planned to follow protein-ligand tutorial. Unfortunately ended up with an error in gro file format. Have check every possibility but still couldn't find any solution. My initial pdb is water.pdb and the corresponding gro file is water.gro. I clubbed the ligand gro file and water gro file as complex.gro. I have uploaded the file here. can anyone help me with the format issues>? -- *Regards,* *Rahul * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx hbond query
Make index of water mediated hydrogens and DNA bases so that DNA bases are in separate group and water mediated hydrogens in separate group in drop down menu On Thu, May 9, 2019, 11:54 AM wrote: > Dear all > I want to determine the water mediated hydrogen between DNA bases and > small molecule. What extra flag should I use in gmx hbond command? Is > there any other option to capture the water mediated Hbonds? Please > suggest something. > Sunipa Sarkar > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs2018.5 install with gaussian09 for QM/MM
Hi, I think it will still work if you use the "gau": script found here: http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian best, Gerrit On 5/7/19 9:59 PM, ??? wrote: > Dear Gromacs support, > I want to install Gromacs 2018.5 with gaussian09 software support in Centos > system, I try to use ?--with-qmmm-gaussian? when I compile gromacs, but it > does not work. I wonder how to compile gromacs with gaussian support, please > help me ? > > > The detail command is as follows: > > cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs \ >-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx \ >-DGMX_OPENMP=ON \ >-DGMX_FFT_LIBRARY=fftw3 \ >-DFFTWF_LIBRARY="/opt/fftw-3.3.8/lib/libfftw3f.a" \ >-DFFTWF_INCLUDE_DIR="/opt/fftw-3.3.8/include/" \ >-DGMX_MPI=on \ >-DGMX_CPU_ACCELERATION=AVX_256 \ >--with-qmmm-gaussian \ >2>&1 | tee cm.log > Gromacs 2018.5 compile and install successfully without ?--with-qmmm-gaussian > \? That's extremely old syntax using the autoconf build system. What you want is -DGMX_QMMM_PROGRAM=GAUSSIAN, but be aware that the QM/MM interface in GROMACS is unmaintained and may not even currently work. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx hbond query
Dear all I want to determine the water mediated hydrogen between DNA bases and small molecule. What extra flag should I use in gmx hbond command? Is there any other option to capture the water mediated Hbonds? Please suggest something. Sunipa Sarkar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Implicit Solvent with User Defined Potentials
Den 2019-05-08 kl. 16:21, skrev Akash Banerjee: Dear Gromacs Developer, I want to use the implicit solvent (gbsa algorithm) along with User-defined tabulated potentials. Apparently, the implicit solvent option is not compatible with the vdw-type=USer option. Can I please get some advice on this? Thank you for your help. Kind regards, Akash GB has been removed from GROMACS and if old versions do not have this option it seems you are out of luck. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
