Re: [gmx-users] 2019.2 build warnings

Just to update: we rolled back to 2018.1 due to a new simulation, which is running perfectly fine on the older version. The only difference between this simulation and everything we've tried so far is that each charge value in the topology (for about 3000 atoms) has something like five digits

[gmx-users] Energy conservation problem in NVE simulation for a system with frozen atoms

Hi all, I am simulating a system with two slabs and water molecules in between. The slabs were frozen during simulations and I've exclude the interactions between slab atoms. After energy minimization, I run nvt at 300 K for 10 ns, followed by annealing the system to 250 K in 1 ns. Then another

[gmx-users] 2019.2 not using all available cores

gmx 2019.2 compiled using threads only uses a single core mdrun_mpi compiled using MPI only uses a single core, gmx 2016.3 using threads uses all 12 cores. For compiling thread version of 2019.2 used: cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs-2019.2 For compiling

[gmx-users] How to calculate Stress Strain curve in GROMACS

Dear GROMACS users, I’m currently running GROMACS to simulate a simple phospholipid bilayer membrane (POPC) under deformation, and plot the von Mises stress-strain curve to determine yielding point. Hence, how can I obtain stress strain value to plot the curve for a deformed membrane in

[gmx-users] Error in mdrun

Hi allI am trying to run md simulation of a 83 residue protein with AMBER99SB-ILDN protein forcefield and TIP3P water model, i am adding orientation restraint to my protein alone however when i run NVT equlibration i get this errorFatal error: Found 5384 copies of a molecule with orientation

Re: [gmx-users] Pressure coupling in expanded ensemble simulations

Yeah, this is an unfortunately place in the code where not all combinations work - very long story. Hopefully this will be working better in 2020. What I would recommend is, if possible, performing the expanded ensemble simulation at NVT. Everything should work fine there (paper coming out

Re: [gmx-users] Using grace in windows

Hi, You can use qtGrace in Windows directly. Regards, Subhomoi B. On Wed, May 8, 2019, 7:14 PM DEEPANSHU SINGLA wrote: > I am trying to plot graph from gromacs generated xvg files in windows 10 > using Linux subsystem command line. I installed grace using the same > command line. When I try

[gmx-users] About densmap tool

Hello, I am working with a membrane protein inserted in a heterogeneous bilayer, with different lipids at different ratios. I used gmx densmap to obtain 2D maps of the lipids distribution, based in the PO4 group. I use the command as following: gmx densmap -s -f -n -od -unit nm-2 -bin

Re: [gmx-users] Using grace in windows

Thank you Mr. Micholas D. for the reply. Sir is it possible to use qtgrace by using linux subsystem command line. If so then can you please tell me the commands to do so. Deepanshu On Wed, 8 May 2019, 19:14 DEEPANSHU SINGLA, wrote: > I am trying to plot graph from gromacs generated xvg

[gmx-users] Implicit Solvent with User Defined Potentials

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

[gmx-users] Pressure coupling in expanded ensemble simulations

Hi all: We are interested to do expanded ensemble simulations (such as simulated tempering) on GROMACS.  Extensive fiddling with the settings and googling on other people's experience suggests that these simulations must use the md-vv integrator, which in turn is compatible with Berendsen or

Re: [gmx-users] Using grace in windows

This is more of a linux subsystem question than a gromacs question; however, you may want to know that there is a native grace for windows: qtGrace (its on source-forge). Not exactly the same as grace, but works really well. -Micholas === Micholas Dean Smith, PhD. MRSC

[gmx-users] Using grace in windows

I am trying to plot graph from gromacs generated xvg files in windows 10 using Linux subsystem command line. I installed grace using the same command line. When I try to plot the graph using grce in the command line by using the following command : xmgrace filename.xvg I get the following

Re: [gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

Thank you Justin sir for the reply. I have resolved my problem. On Wed, May 8, 2019, 5:57 PM Justin Lemkul wrote: > > > On 5/7/19 1:41 AM, ISHRAT JAHAN wrote: > > -- Forwarded message - > > From: ISHRAT JAHAN > > Date: Tue, May 7, 2019 at 11:05 AM > > Subject: atoms are not

Re: [gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

On 5/7/19 1:41 AM, ISHRAT JAHAN wrote: -- Forwarded message - From: ISHRAT JAHAN Date: Tue, May 7, 2019 at 11:05 AM Subject: atoms are not part of any of the T-Coupling groups To: Dear all, I am trying to calculate the lennard Jones interaction energy between protein and

Re: [gmx-users] Gromacs2018.5 install with gaussian09 for QM/MM

On 5/7/19 9:59 PM, 辛志宏 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 ?

Re: [gmx-users] How to calculate tetrahedral order parameter in GROMACS

Thanks. I am checking. On Wed, 8 May 2019, 2:30 pm David van der Spoel, wrote: > Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: > > Hello, > >I have two systems. One containing only water and the other one > > contains protein and water. Using g_select I made water in 1st solvation > >

Re: [gmx-users] How to calculate tetrahedral order parameter in GROMACS

Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: Hello, I have two systems. One containing only water and the other one contains protein and water. Using g_select I made water in 1st solvation shell but the use of g_hydorder I cannot understand. I read the disscussion so far disscussed. For