Re: [gmx-users] mdrun error

Dear Golnaz, Depending on how your system is set up, you have a few options, listed here in the order I would try them (knowing no details about your system): 1) If you have less than, say, 100~500 atoms per CPU core (depending on your network), use less nodes to run the simulation. The

Re: [gmx-users] service broken?

Hi, I just tried and had no problem, so maybe it's some setting on your end? Otherwise, it would be more appropriate to contact the MacKerell group about this and not the gromacs list: a...@outerbanks.umaryland.edu Regards, Peter -Original Message- From:

[gmx-users] removing some atoms

Hi all, I have a oil slab and want to insert a protein so that almost half of the protein is inserted into the oil and the other half is outside in the vacuum. Is there any tools in Gromacs so that I can easily remove some of the oil atoms and make a space for the protein insertion? My apology if

Re: [gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force

Maybe someone has an idea how to extract the instantaneous forces from the trajectory. I would normally use g_traj command to extract the forces however I am not sure if this force means instantaneous force. On Wed, Nov 25, 2015 at 2:02 PM, gozde ergin wrote: > Dear

[gmx-users] mdrun error

Dear users I got this error in my mdrun There is no domain decomposition for 4 nodes that are compatible with the given box and a minimum cell size of 7.1147 nm. my system contains graphene and surfactants. In last box I put graphene in the middle of my box and the graphene was npbc and the mdrun

[gmx-users] Umbrella sampling force autocorrelation

Dear Gromacs user, I did umbrella sampling by pulling a water molecule from gas phase to organic coated bulk water. By clicking the link below you can see my PMF profile. In order to estimate the transmission coefficient, I put the pulled molecule on the top of the PMF barrier and did simulation

[gmx-users] Problem compiling 4.6.7 with gpu support

Hi, I am trying to compile gromacs 4.6.7 on a notebook with two gt 650m , ubuntu 15.10 and cuda 7.0 installed. On my system are installed gcc 4.8 4.9 and 5.2 For the gpu support I use the following: cmake .. -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON

Re: [gmx-users] Problem compiling 4.6.7 with gpu support

Hi, CUDA 7.0 supports gcc 4.9 and earlier as you can see stated in the docs as well as in the somewhat awkward error message that originates from the include/host_config.h:105 header. I think you did not correctly set up your build to use gcc 4.8 or 4.9 and you are simply using your system

[gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution?

Dear expert, My molecular dynamics simulation was performed in 1.5 M KCl aqueous solution or 1.5 M KCl ethanol solution (v:v=1:1). The oplsaa force field and spc216.gro were used (300k,1bar). The results showed that KCl aggregated with 10 ns of simulation. Could you tell me why the aggregate