[gmx-users] N-acetyl-d-glucosamine parameters

Hi all! I want to do a simulation of a protein that have a disaccharide (formed by two units of the N-acetyl-d-glucosamine) covalently bonded to the L-asparagine amido group of the protein. Is there an adequate force field in gromacs for dealing with N-acetyl-d-glucosamine? Any help would be app

Re: [gmx-users] GPU slower than I7

. */ #define HAVE_GETTIMEOFDAY /* Define to 1 if you have the cbrt() function. */ #define HAVE_CBRT . . . Is this OK? Renato 2010/10/22 Roland Schulz : > Hi, > > On Fri, Oct 22, 2010 at 3:20 PM, Renato Freitas wrote: >> >> Do you think that the "NODE" and "Real&quo

Re: [gmx-users] GPU slower than I7

is that you would be better off > using the standard mdrun which in 4.5 by default has thread-support > and therefore will run on a single cpu/node without MPI! > > Cheers, > -- > Szilárd > > > > On Thu, Oct 21, 2010 at 9:18 PM, Renato Freitas wrote: >> Hi gromacs us

Re: [gmx-users] GPU slower than I7

. About the CPU vs GPU simulation time, Szilárd explained that the PME algorithms still are not very well suited for current GPU architectures. I just don't know why the NODE and REAL times are not equal. Thanks, Renato 2010/10/21 Roland Schulz : > > > On Thu, Oct 21, 2010 at 5

Re: [gmx-users] GPU slower than I7

that with GPU. It seems correct to you? As I said before, I was expecting that GPU should take a lower time than the 6 core MPI. Thanks, Renato 2010/10/21 Roland Schulz : > > > On Thu, Oct 21, 2010 at 3:18 PM, Renato Freitas wrote: >> >> Hi gromacs users, >> >

[gmx-users] GPU slower than I7

Hi gromacs users, I have installed the lastest version of gromacs (4.5.1) in an i7 980X (6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its mpi version. Also I compiled the GPU-accelerated version of gromacs. Then I did a  2 ns simulation using a small system (11042 atoms)  to co

Re: [gmx-users] mdrun-gpu error

Hi Roland, I did as you suggested and it worked fine! Thanks, Renato 2010/10/15 Roland Schulz : > You should use the latest GROMACS version also for the GPU. Thus compile the > 4.5.1 for the GPU and run this. > > On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas wrote: >>

[gmx-users] mdrun-gpu error

Hi there, I have installed the gromacs-4.5.1 and it was running without problems. Also I installed the GPU version of GROMACS (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and NVIDIA driver are installed. Then I tried to run the test provided by Alan with the mdrun-gpu and I got