Re: [gmx-users] using dual CPU's

> On Dec 10, 2018, at 7:33 PM, paul buscemi wrote: > > > Mark, attached are the tail ends of three log files for > the same system but run on an AMD 8 Core/16 Thread 2700x, 16G ram > In summary: > for ntpmi:ntomp of 1:16 , 2:8, and auto selection (4:4) are 12.0, 8.8 , and > 6.0 ns/day. >

Re: [gmx-users] Does adding artificial mass cause problems for friction studies?

Look into heavy hydrogens (x4 mass) which is one way to increase the time step since the frequency of vibrations for the hydrogen bond is decreased due to the increase in mass. Should be a number of references out there looking into the effect the mass increase has directly. Catch ya, Dr.

[gmx-users] Gmx gangle

Hi, I don't really understand how gmx gangke works!!! I want to calculate angle between amino acid ring and surface during simulation. I mad3 an index for 6 atoms of ring(a_CD1_CD2_CE1_CE2_CZ_CG) and two atoms of surface. Surface is in xy plane and amino acid is in different Z distances. I

Re: [gmx-users] problem with introducing a new structure in gromacs, please help if anybody knows

The overall charge for an entire molecule has to be an integer value, anything other than that is physically impossible. So you have to fix your charges so that is the case, and you must have done something wrong where you pull/calculated the charges. Catch ya, Dr. Dallas Warren Drug Delivery,

Re: [gmx-users] using dual CPU's

Mark, I may have misread the ppt on optimization, but I did experiment with variations of mtomp mtmpi and so using less than si x threads was a 2 x 3 combination. Tonight I will put both this is the last part of the log from a 2 gpu setup using gmx

[gmx-users] Does adding artificial mass cause problems for friction studies?

Hi, When studying friction it can be inconvenient for a structure to have low mass. If you push on the structure hard enough to overcome static friction, it then accelerates so rapidly that the speeds are unrealistic. One way to overcome this problem is to increase the structure's mass. But,

Re: [gmx-users] using dual CPU's

Hi, One of your reported runs only used six threads, by the way. Something sensible can be said when the performance report at the end of the log file can be seen. Mark On Tue., 11 Dec. 2018, 01:25 p buscemi, wrote: > Thank you, Mark, for the prompt response. I realize the limitations of the

Re: [gmx-users] Mean square displacement on Log-Log plot?

Den 2018-12-10 kl. 21:57, skrev Kevin Boyd: Hi, If you're reporting a diffusion coefficient, they're probably looking for you to justify that you're out of the short-time subdiffusive regime. My experience is in bilayer simulations, where the MSD hits that regime typically in the time lag range

Re: [gmx-users] Mean square displacement on Log-Log plot?

Hi, If you're reporting a diffusion coefficient, they're probably looking for you to justify that you're out of the short-time subdiffusive regime. My experience is in bilayer simulations, where the MSD hits that regime typically in the time lag range of ~10-20 ns. For a qualitative estimate of

[gmx-users] Mean square displacement on Log-Log plot?

Hi, unusual request, but here goes. I am dealing with a referee to one of my papers who is asking for a mean square displacement plots: "a log-log plot of the MSD vs. time, from which one could judge whether the long-time limit subject to multiple collisions and obstructions is actually

[gmx-users] Buckingham potential

Hi, I want to use both Buckingham potential and LJ in a same simulation since using table potential are slow. Do you have any suggestion how to incorporate both potentials in the simulation. Best, Hosein -- Gromacs Users mailing list * Please search the archive at

[gmx-users] problem with introducing a new structure in gromacs, please help if anybody knows

Hi there, I'm working on MOFs ( metal organic frameworks) with gromacs, before starting the simulation, I should introduce my molecule in aminoacids.rtp file, that I did it, my problem is I have 4 repetitive structures (Ligands) and 2 metals, the whole charge of molecule is zero but every one of

Re: [gmx-users] Install GROMACS 2018 with CUDA features in dynamic linking way

On Sat, Dec 8, 2018 at 10:00 PM Gmail wrote: > > My mistake! It was a typo. Anyway, this is the result before executing > the chrpath command: > > chrpath -l $APPS/GROMACS/2018/CUDA/8.0/bin/gmx > $APPS/GROMACS/2018/CUDA/8.0/bin/gmx: RPATH=$ORIGIN/../lib64 > > I'm suspicious that GROMACS 2018 is

Re: [gmx-users] using dual CPU's

Thank you, Mark, for the prompt response. I realize the limitations of the system ( its over 8 yo ), but I did not expect the speed to decrease by 50% with 12 available threads ! No combination of ntomp, ntmpi could raise ns/day above 4 with two GPU, vs 6 with one GPU. This is actually a

Re: [gmx-users] mdrun-adjusted cutoffs?!

On Mon, Dec 10, 2018 at 6:57 AM Mark Abraham wrote: > > Hi, > > There's two ways to specify the long-range grid requirements (either > fourierspacing, or fourier-nx and friends,, see > http://manual.gromacs.org/documentation//current/user-guide/mdp-options.html#ewald). > The tuning will override