Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

I apologize for the confusion, but I found my error. I was failing to request a certain number of cpus-per-task and the scheduler was having issues assigning the threads because of this. Speed is now at ~400 ns/day with a 3 fs timestep which seems reasonable. Thanks for all the help, Dan On Wed,

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Szilárd, I think I must be misunderstanding your advice. If I remove the domain decomposition and set pin on as suggested by Mark, using: gmx_gpu mdrun -deffnm my_tpr -dd 1 -pin on Then I get very poor performance and the following error: NOTE: Affinity setting for 6/6 threads failed. This can

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Hi, Replying to say thanks and add a few details in case anyone comes across this thread in a search. Setting LD_LIBRARY_PATH did the trick. On Ubuntu 17.04 that’s /usr/lib/gcc/x86_64-linux-gnu. Also, I had to install gcc-5 and g++-5 again because the CUDA 8 toolkit doesn’t like version 6,

[gmx-users] simulating AMP covalently linked to a protein

Hi, I'm interested in simulating a DNA ligase with an AMP bound covalently via its P atom to the side chain of a Lysine residue. I can not find any parameters for that. I really appreciate any help in how to achieve this. thanks in advance, Gilberto -- Gromacs Users mailing list * Please

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

+ let me emphasize again what Mark said: do not use domain-decomposition with such a small system! All the overhead you see comes from the communication you force mdrun to do by running multiple ranks. BTW the 1.1 us/day number you quote does a ~6000 atoms simulation with 4 or 5 fs time-step (so

Re: [gmx-users] sequential simulations with mdrun -multi option

You're choosing 240 ranks for 20 simulations, so that is 12 ranks per simulation. Start 20 ranks for your position-restrained simulation, to avoid this historical mal-implementation. Mark On Wed, 24 May 2017 17:15 Debdip Bhandary wrote: > > Dear Users, > I am

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Hi, I'm wondering why you want 8 ranks on the 14 or 28 cores. The log reports that something F else is controlling thread affinity, which is the easiest thing to screw up if you are doing node sharing. The job manager has to give you cores that are solely yours, and you/it need to set the

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Thanks so much for the quick reply. That seems to have fixed the wait time issues. Unfortunately, I'm still only getting ~300 ns/day for the benchmark system (villin vsites, http://www.gromacs.org/GPU_acceleration), while the website claims over 1000 ns/day. I'm running on a NVIDIA Tesla

[gmx-users] RMSF per residue

Dear Gromacs users, I have a question on RMSF calculation: I am not sure how -res works in RMSF and I could not find any useful explanation for it. It will give the average fluctuations per residue, fine. but how exactly? 1) it calculates the RMSF for each atom in that residue first. Then, it

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Try just using your equivalent of: mpirun -n 2 -npernode 2 gmx_mpi mdrun (your run stuff here) -ntomp 4 -gpu_id 00 That may speed it up. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular

[gmx-users] Poor GPU Performance with GROMACS 5.1.4

Hello, I'm using GROMACS 5.1.4 on 8 CPUs and 1 GPU for a system of ~8000 atoms in a dodecahedron box, and I'm having trouble getting good performance out of the GPU. Specifically it appears that there is significant performance loss to wait times ("Wait + Comm. F" and "Wait GPU nonlocal"). I have

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Thanks Justin! It worked. All bonds are now in place. I’ll play with the branching a bit and will make a new ticket, if I had a problem. Thank again, MH > On May 24, 2017, at 1:04 PM, Justin Lemkul wrote: > > > > On 5/24/17 12:04 PM, Mohammad Hassan Khatami wrote: >> Sorry

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

On 5/24/17 12:04 PM, Mohammad Hassan Khatami wrote: Sorry for that. Here are the types. atom type C1 CC3162 O4 OC311 O4 should be OC301 for all 1-4 linkages (PRES 14aa, 14ab, 14ba, 14bb in top_all36_carb.rtf). -Justin C4 CC3161 C5 CC3163 C3 CC3161 H4

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Sorry for that. Here are the types. atom type C1 CC3162 O4 OC311 C4 CC3161 C5 CC3163 C3 CC3161 H4 HCA1 I checked them, but I was not able to find the exact combination of atoms angles and dihedrals associated with them in the ffbonded.itp. For example,

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

On 5/24/17 11:35 AM, Mohammad Hassan Khatami wrote: On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami wrote: Some how I figured out the problem and fixed it! I changed "O4 +C1" to "O4 2C1” and it worked. I hope it is correct. Nope! the bond are not made this

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

> On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami wrote: > > Some how I figured out the problem and fixed it! I changed "O4 +C1" to > "O4 2C1” and it worked. I hope it is correct. Nope! the bond are not made this time! That’s why grompp did not complain! > Now I

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Some how I figured out the problem and fixed it! I changed "O4 +C1" to "O4 2C1” and it worked. I hope it is correct. Now I have to move on to make the more complicated form of my polymer, and add 1->6 connection to the system, like below:

[gmx-users] sequential simulations with mdrun -multi option

Dear Users, I am trying to perform n number of simulations in parallel using -multi option with mdrun (version 5.0.4). I want to simulate the system at different conditions in parallel using '-multi' option. The process involves nvt followed by NpT step. The jobscript is as following:

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

That should not be needed if this is a default Ubnutu 17.04 install that comes with gcc 6 ootb, I think. -- Szilárd On Wed, May 24, 2017 at 2:13 PM, Mark Abraham wrote: > Hi, > > Using a gcc version also entails linking to the standard library that comes > along with

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Hi Justin, Here are all the errors with the (atom indices) and the "atom names”. Based on the order of the errors I think I am making mistakes when I am trying to modify the AGLC units to connect them through O4-2C1 (O4 to the C1 of the next residue). I am some how sure that I am making

Re: [gmx-users] high temperature during mdrun

On 5/24/17 8:52 AM, fatemeh ramezani wrote: Hi dear gmx-usersI am simulating gold surface- protein interaction by GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun starts, temperature

Re: [gmx-users] Need to confirm parameters.

On 5/23/17 11:06 PM, Sailesh Bataju wrote: * Making bonds... *>>* Warning: Short Bond (5-1 = 0.025 nm) *>>* Warning: Long Bond (5-6 = 0.99084 nm) *>>* Warning: Long Bond (1-2 = 0.944378 nm) *>>* Warning: Long Bond (1-3 = 0.895661 nm) *>>* Warning: Long Bond (1-4 = 0.866986 nm) *>>*

[gmx-users] high temperature during mdrun

 Hi dear gmx-usersI am simulating gold surface- protein interaction by GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun starts, temperature reaches to 5.50769e+05 and mdrun fails. md.mdp

Re: [gmx-users] gromacs-5.1.4 installation issue

This kind of issues can mean that you moved compiled binary to quite different machine. Though I am not sure what you did. Compile on the same machine you are going to use or at least as similar as possible (same Linux ver. with same updates). On Wednesday, May 24, 2017 3:13 PM, abhisek

Re: [gmx-users] gromacs-5.1.4 installation issue

Hi, You should ask the cluster maintainers how they intend the compiler to be used. You need to find the same infrastructure at run time as you used at compile time, e.g. by loading the same modules. Mark On Wed, May 24, 2017 at 2:13 PM abhisek Mondal wrote: > Hi, > >

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Hmm It might be problem that you removed compilers. Wonder what you have now.If you still have problem please post output of: g++ -v && gcc -v Command. On Wednesday, May 24, 2017 3:14 PM, Mark Abraham wrote: Hi, Using a gcc version also entails linking to

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Hi, Using a gcc version also entails linking to the standard library that comes along with it, ie libstdc++.so. By default, it will link at run time to the version that shipped with the package. For any sufficiently new compiler, that won't work (by design) because the library and the compiler

[gmx-users] gromacs-5.1.4 installation issue

Hi, I have been trying to install latest version of gromacs (Gromacs-5.1.4) in my cluster. Installation went without any error. But whenever I'm giving the command: gmx_mpi An error report comes: gmx_mpi: /lib64/libz.so.1: no version information available (required by

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Hi Vytautas, I should have mentioned that I had deleted the ‘build’ directory and tried the cmake command again, but I received the same error. I had installed a large number of different compilers (clang-3.8, clang-4.0, gcc-5) to get my CUDA installation to work but thought I had removed them

[gmx-users] Problem with accelerations

Mark, I'm not really sure what you mean by technique. I assume NEMD stands for Non-equilibrium MD? That is the case in my simulation.. About my simulation: I am trying to simulate a fluid flow between surfaces. Two atomistic surfaces of gold atoms have been created at Z=0 and Z=z, where z is the

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Ubuntu 17.04 should give you quite up-to date gcc and co. Make sure you try this on clean folder: remove everything download and try again. Maybe some old files interfering. On Wednesday, May 24, 2017 4:14 AM, Steffen Graether wrote: Hi, I’ve tried installing