[gmx-users] Why does "system is not well equilibrated" error come out when using multiple GPUs but not one GPUs?

Dear everyone, I am trying to run a MD simulation with gromacs-2019.3 on a workstation with multiple GPUs. When I run the simulation with only one GPU by the command: mpirun_mpi -np 1 gmx_mpi mdrun -ntomp 6 -gpu_id 0 -v -deffnm md it can run normally. However, when I try to run the

Re: [gmx-users] pressure is coming 1.39

For two examples that show this, see https://twitter.com/dr_dbw/status/968624615063937025 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

Re: [gmx-users] pressure is coming 1.39

Den 2019-09-08 kl. 06:36, skrev Bratin Kumar Das: Thanks sir for your reply. My target pressure was 1 atm.. The fluctuations depend on the system size as 1/sqrt(natoms). To obtain a std dev of 3 bar you need a really big system. On Sat 7 Sep, 2019, 8:15 PM Mark Abraham, wrote: Hi, Without

[gmx-users] REMD

Hello gmx users, I am getting an error "load imbalance " in remd nvt equilibrium step. Can anyone help me regarding this issue? 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

[gmx-users] Cannot run short-ranged nonbonded interactions on a GPU

Hi With the following config command cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=`pwd`/../single -DGMX_BUILD_OWN_FFTW=ON I get the following error for "gmx mdrun -nb gpu -v -deffnm inp_nvp" Fatal error: Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.

[gmx-users] (no subject)

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[gmx-users] Obtaining AMBER parameters for Mn2+ and zwitterion form Arginine

Hi, I have found a AMBER database with the Mn2+ ion and Arginine (zwitterion) from the following link: http://research.bmh.manchester.ac.uk/bryce/amber How can I convert these parameters so that I can use them in Gromacs. Any help would be much appreciated. Best wishes, Akash -- Gromacs

[gmx-users] Add MSVC binary and build method on MSVC Re: gromacs binaries for windows (Cygwin 64)

- Original Message - > From: Tatsuro MATSUOKA > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Cc: > Date: 2019/9/6, Fri 12:33 > Subject: [gmx-users] gromacs binaries for windows (Cygwin 64) > > I have prepared gromacs binaries for windows (Cygwin 64) on my own web site. >