Re: [gmx-users] gromacs binaries for windows (Cygwin 64)

> -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > Tatsuro MATSUOKA > Sent: Tuesday, September 10, 2019 8:26 PM > To: gmx-us...@gromacs.org; Szilárd Páll ; > tmaccha...@yahoo.co.jp >

Re: [gmx-users] Fat-bottom restrain

Thanks Billy, > If the flat bottom restraint energy is zero, then that means that the > restraints aren't being applied, or your predefined distance is not being > exceeded. I doubt you would get binary zero values if it was the second > option, so something is probably wrong with your syntax or

Re: [gmx-users] optimizing GAFF2 torsional parameters

Hi, I do not have answers to your questions. Just in case you do not know, Junmei Wang and David Case (GAFF developers) follow the Amber reflector: AMBER Mailing List See ambermd.org for subscription info. scott On Mon, Sep 09, 2019 at 09:31:21AM -0500, Christos Deligkaris wrote: > I am

Re: [gmx-users] gromacs binaries for windows (Cygwin 64)

>> As in message in the cmake configure process, gcc on 64 bit windows is > buggy >> for AVX simd instruction. > > Correct. But that is a GCC bug > (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=54412 ) > With ICC, MSVC, and Clang the problem doesn't exist. I also noticed that. I tried build

Re: [gmx-users] Fat-bottom restrain

Hi, It's certainly conceivable that such restraints are ineffective in some run modes. However, "on the GPU" describes a range of scenarios. If you're running with 2019.x, does adding -bonded cpu to the mdrun command line restore the functionality? Otherwise, please try the "working CPU" run on

[gmx-users] How can Build gromacs using MSVC on Win64 with AVX2?

On GROMACS 2019.3, GROMACS cannot be built with AVX2. In gmxSimdFlags.cmake     SIMD_AVX2_C_FLAGS SIMD_AVX2_CXX_FLAGS     "${TOOLCHAIN_FLAG_FOR_AVX2}" "-mavx2" "/arch:AVX" "-hgnu") # no AVX2-specific flag for MSVC yet If I modify the above, "/arch:AVX" => "/arch:AVX" , -- Performing

Re: [gmx-users] How can Build gromacs using MSVC on Win64 with AVX2?

Hi, Those are kernels for legacy code that never use such simd anywhere Mark On Thu., 12 Sep. 2019, 07:16 Tatsuro MATSUOKA, wrote: > On GROMACS 2019.3, GROMACS cannot be built with AVX2. > > In gmxSimdFlags.cmake > > SIMD_AVX2_C_FLAGS SIMD_AVX2_CXX_FLAGS >

Re: [gmx-users] Using -multidir option on Cray (aprun)

Dear all, I have managed to resolve this issue, which was a shell scripting mistake. My mistake was to keep "-multidir remd_{1..2}" inside quotes, hence the Bash expansion of remd_{1..2} did not work as intended. Instead, "-multidir $(echo remd_{1..2})" works. But if anybody has any better

Re: [gmx-users] Fat-bottom restrain

If the flat bottom restraint energy is zero, then that means that the restraints aren't being applied, or your predefined distance is not being exceeded. I doubt you would get binary zero values if it was the second option, so something is probably wrong with your syntax or your inclusion of the

Re: [gmx-users] Fat-bottom restrain

Hi, Any comment, please? Thank you. Alex On Mon, Sep 9, 2019 at 10:22 PM Alex wrote: > Hi Mark, > > Thank you for your response. > Here are the part of options that gmx energy gives me out: > > 9 Coulomb-(SR)10 Coul.-recip. > 11 Flat-bottom-posres

[gmx-users] Steered MD:Setup box in the pulling vector direction and position restraint for protein?

I want to setup a steered molecular dynamics to pull a ligand out of protein binding site. I used caver to determine an ‘optimal’ pulling direction for the protein-ligand complex. Now I am to enlarge the simulation box in that direction. For now, this is the command I am using: gmx editconf -f

[gmx-users] Using -multidir option on Cray (aprun)

Hello! I am trying to use the -multidir feature of mdrun for setting up a REMD simulation on a Cray XT system. It requires the "aprun" launcher to spawn the parallel processes rather than the usual mpirun (which I have successfully used with -multidir before). I am using the 2019.3 version of

Re: [gmx-users] Fat-bottom restrain

You may want to consider using smart-bottom restraints instead? Jokes aside, why does it matter if your molecules move into the next periodic image? Cheers, Billy On Wed., 11 Sep. 2019, 5:03 pm Alex, wrote: > Hi, > > Any comment, please? > > Thank you. > Alex > > On Mon, Sep 9, 2019 at 10:22

Re: [gmx-users] How to use gmx h2order when using four point water model

Den 2019-09-11 kl. 04:38, skrev Jun Zhou: Hi all, I want to obtain the water dipole orientation at the interface using gmx h2order. It works well when I I use 3 point water model, like SPC/E. The manual says that the order of water should be O H H, but for 4 point water model, there is a vitual

Re: [gmx-users] Delete Groups from gro file

Hi Larissa, `gmx editconf` should do what you need for gro files; `gmx trjconv` for trajectories. Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Gselman, Larissa Sent: Wednesday, September 11, 2019 12:10 PM To: gmx-us...@gromacs.org

Re: [gmx-users] Using -multidir option on Cray (aprun)

Hi, Putting the mdrun_mpi command into a variable makes sense, but the rest of the command line makes sense directly, so you get the shell expansions you might intend. Mark On Wed, 11 Sep 2019 at 08:53, Suman Chakrabarty wrote: > Dear all, > > I have managed to resolve this issue, which was a

[gmx-users] Delete Groups from gro file

Hallo All, I have a big gro file with 10 different groups. For my simulation, I only need one (Group 6) of them in a new gro file. So, how can I make this new gro file? I made an index file with this command: gmx_mpi make_ndx -f membrane.gro -o membrane.ndx and selected my group with „keep

Re: [gmx-users] Domain decomposition error while running coarse grained simulations on cluster

> > Here's your problem. You have pairs defined that are in excess of 12 nm, > but they are assigned to a 1-4 interaction, so atoms that should be > separated by three bonds. The user-defined potential shouldn't matter > here unless you've added [pairs] to the topology. > > I see your point. What

Re: [gmx-users] Delete Groups from gro file

Hi, You could use gmx trjconv: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html You can use the index file to select only that subset of atoms from a single frame of your trajectory and output it as a new .gro file. Cheers, John > Hallo All, > > I have a big gro file

[gmx-users] Ramachandran Plot for a Polymer

Dear Gromacs Users, Can we get the Ramachandran plot for a polymer using Gromacs? If we can, how do we do that? Appreciate your help. Thank you. -- Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] [EXTERNAL] Ramachandran Plot for a Polymer

gmx chi or gmx rama may work. I have used these for proteins, but it would be worth looking at the code to see if it would also work for polymers in general. -Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National

[gmx-users] compressibility

Dear Justin,I'm simulating 400 molecules of naphthalene in NPT ensemble at gas phase. Is it true that I set water compressibility in .mdp file? What must I do? Should I look for naphthalene isothermal compressibility in articles to use it?Thanks,Sana -- Gromacs Users mailing list * Please

[gmx-users] SMD options

Hi all, following my previous post regarding anomalous behavior of gromacs on running with two gpus, I have some new elements to add. I tested the workstation with two tools for gpu and cpu I found on the web (gpu_burn and stress); I ran the two of them at the same time for two hours pushing both

[gmx-users] Fwd: query

Hello, I want to calculate the energy of the two groups. I have defined those groups in mdp file. I want to run it for 5 ns. So, I set the nsteps and all parameters according to my need. Now I am using the rerun command for calculating the energy. But it is only giving the energies till 100 ps