[gmx-users] uni axial deformation with semi-isotropic pressure coupling at 1 bar

Dear all, While using 'deform' option for elongation in Z direction, I have set the compressibility to zero. Should I set pressure in z direction also zero (ref_p =0 ) or 1 in that direction. I need to extract -Pzz for plotting stress-strain. Thanks -- Gromacs Users mailing list * Please se

[gmx-users] Fwd: Which output of gmx energy represents stress

Dear all, I am calculating stress-strain using uniaxial deformation with deform option. Which output of gmx energy represents stress *Is it Press-XX or VIR-XX,* or some other value.(supposing the deformation is in x direction) Thanks in advance, Pragati -- Gromacs Users mailing list * Please s

[gmx-users] Which output of gmx energy represents stress

Dear all, I am calculating stress-strain using uniaxial deformation with deform option. Which output of gmx energy represents stress *Is it Press-XX or VIR-XX,* or some other value.(supposing the deformation is in x direction) Thanks in advance Pragati -- Gromacs Users mailing list * Please se

[gmx-users] Uniaxial elongation using deform option

Dear all, I want to calculate young's modulus of a polymer using uniaxial elongation. (elongation in z axis but no volume change) I am using 'deform' option and semiisotropic pressure coupling and zero compressibility in z for that. My mdp parameters ar: *Pcoupl = Beren

[gmx-users] Cut off (1.2 -1.5 nm) with OPLS forcefield

Hello all, I am simulating a polymeric system using OPLS-AA forcefield. I can see a considerable change in density while changing the cut off from 1.2 to 1.5 nm cut off Density Experimental density 1.2895 kg/m3910-9

[gmx-users] specific heat calculation using "gmx dos"

Dear all, I am trying to calculate heat capacity of a polymeric system (30k atoms) using gromacs. I tried the classical way from the fluctuation dependent properties using "gmx energy", but the values are not matching experimental values. I want to use "gmx dos" program, but I have some confusio

[gmx-users] Force (%)" value in md.log file

Hello all, I am simulating a polymer system (3 atoms, 2fs time step, PME) on a workstation with CPU: 2X6 cores (24 logical) and 2 2080 RTX GPUs. I am running the 2 separate simulations using 10 threads and 1 GPU each using command: *gmx_tmpi mdrun -v -deffnm md2 -nb gpu -gpu_id 1 -nt 10* I

Re: [gmx-users] Groms 2019.0, simulations using 2 GPUs: RTX 2080Ti

t; > > > For running different simulations on your GPUs, you need to set the > > environment variable CUDA_VISIBLE_DEVICES so that each simulation only > > sees on of the available GPUs. > > > > Cheers > > > > Paul > > > > On 13/12/20

Re: [gmx-users] Groms 2019.0, simulations using 2 GPUs: RTX 2080Ti

Thanks Nikhil. About the second question. It is actually implemented , as you can see the link below, however I cannot run these commands without error. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-July/126012.html On Fri, Dec 13, 2019 at 12:28 PM Nikhil Maroli wrote: > You

[gmx-users] Groms 2019.0, simulations using 2 GPUs: RTX 2080Ti

Hello all, I am running a polymer melt with 10 atoms, 2 fs time step, PME, on a workstation with specifications: 2X Intel Xeon 6128 3.4 2666 MHz 6-core CPU 2X16B DDR4 RAM 2XRTX 2080Ti 11 GB I have installed *GPU and thread_mpi *enabled gromacs 2019.0 version using: cmake .. -DGMX_BUILD_OWN_

[gmx-users] Calculation of young's modulus from stress-strain plot

Hello users, I am trying to plot stress-strain curve for natural rubber from NPT simulations using the "deform" option. Deform along x direction at 1 bar pressure. The parameters I gave in mdp file are: Pcoupl = Berendsen Pcoupltype = semiisotropic tau_p

Re: [gmx-users] Specific heat calculations using gmx energy

program, it stop with an index error. I will try gmx dos in gromacs 2019 and check the Cp values again. On Wed, Jul 17, 2019 at 1:04 AM David van der Spoel wrote: > Den 2019-07-15 kl. 09:24, skrev Pragati Sharma: > > Dear all, > > > > I am simulating a melt of polybutadi

[gmx-users] Specific heat calculations using gmx energy

Dear all, I am simulating a melt of polybutadiene consisting of 60 chains using OPLS forcefield. After 50 ns of NPT production run, specific heat is calculated using the command: *gmx energy -f ener.edr -fluct_props -nmol 60 -driftcorr * and the value obtained is: Enthalpy

[gmx-users] Transference of dihedral potentials between united atom and all-atom force fields

Hello gromacs users, I have a query regarding transference of dihedral potentials between united atom and all-atom force fields. Suppose, for a dihedral of four carbon atoms in polybutadine (united atoms: CH2-CH=CH-CH2). Can I use the same dihedral potentials or force constants for the same set of

Re: [gmx-users] using GPU acceleration in gromacs

f that GPUs has > been deprecated. > > -- > Szilárd > > > On Fri, May 24, 2019 at 8:59 AM Pragati Sharma > wrote: > > > Hello users, > > > > I am trying to install gromacs-2019 on a HP workstation containing > > NVIDIA-quadro 5000 GPU card. > &

[gmx-users] using GPU acceleration in gromacs

Hello users, I am trying to install gromacs-2019 on a HP workstation containing NVIDIA-quadro 5000 GPU card. I installed gromacs using ‘sudo apt-get install gromacs’ on opensuse. After running a polymer simulation, I checked the log file and it is showing GPU-disabled in Gromacs properties. I nee