[gmx-users] Using Poisson mean field approximation for electrostatic interactions

Hi, My objective is to use Poisson equation based mean field approximation for the electrostatic interactions. So, I need to figure out how to achieve this in Gromacs. I understand PME uses Poisson equation for the long-range component in addition to the direct Coulomb sum for the pairs within a

[gmx-users] non-bonded kernels for water

Hi, I am wondering what non-bonded kernel is used for water simulations when gromacs is built with None SIMD option? Is it plainC or water specific highly optimized kernel? I understand that there are highly optimized kernels specific to water and are they still used even if SIMD=None? Thanks,

[gmx-users] segmentation fault

Hi, I am trying to simulate a confined water system with gromacs 5.0.5, however, I am getting the segmentation fault. Below are the gdb backtrace and the build info. Thanks, Sikandar backtrace:: #0 0x7767d8dd in _mm_loadu_pd (tab_coul_F=0x7fffe6217100, tab_coul_V=0x7fffe621b560,

[gmx-users] neighbor list

Hi, I need to set up a simulation of LJ system, such that neighbor list is built using grid algorithm with a cut-off of lj_cut_off + 0.1 every 20 timesteps. So I am wondering what should be the accurate settings in the grompp.mdp file. After reading the manual, I understand rvdw must be =

Re: [gmx-users] neighbor list

Thanks Mark. That helps. -- Sikandar On Mon, Jul 28, 2014 at 1:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Jul 28, 2014 at 8:27 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi, I need to set up a simulation of LJ system, such that neighbor list is built using

Re: [gmx-users] time accounting in log file with GPU

, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Szilárd. I am bit confused about the -resethway or -resetstep options. Do they exclude the time spent on initialization and load-balancing from the total time reported in the log file, i.e., the time reported is the total time spent

[gmx-users] time accounting in log file with GPU

Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I

Re: [gmx-users] time accounting in log file with GPU

Thanks Mark. -noconfout option helps. -- Sikandar On Thu, Jul 24, 2014 at 3:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple

[gmx-users] coulomb interactions with zero charge atoms

Hi I am wondering if I have a system of simple LJ atoms with no charge on then, will gromacs still compute coulomb interaction computations? Thanks, Sikandar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] condition on MPI and GPU tasks

Hi, I am checking out GPU performance of Gromacs5.0 on a single node of a cluster. The node has two 8-core Sandy Bridge Xeon E5-2670 and two NVIDIA K20x GPUs. My question - is there a restriction on how many number of MPI tasks can be used per GPU task? I observe that I could only perform mdrun

[gmx-users] more than 99,999 atoms in conf.gro

Hi I am trying to run a simulation with more than 99,999 atoms in a conf.gro file. However, when I run grompp I get an error Fatal error: Something is wrong in the coordinate formatting of file conf.gro. Note that gro is fixed format (see the manual) As suggested in the online manual, I am

Re: [gmx-users] more than 99,999 atoms in conf.gro

Thanks Chandan it worked! On Tue, Jul 15, 2014 at 8:56 AM, Chandan Choudhury iitd...@gmail.com wrote: Hi Sikandar, Did you try resetting your atom number to 1 as it reaches 10? I hope this would resolve the issue. Chandan On Tue, Jul 15, 2014 at 3:43 PM, Sikandar Mashayak symasha

Re: [gmx-users] limitation of no. of atoms in the .gro file

-number field. Is that the question you meant to ask? :-) In practice, in making such a file, you should wrap from 99 or whatever to 0, because GROMACS only ever checks to see that the value changes. Mark On Mon, Jul 14, 2014 at 10:13 PM, Sikandar Mashayak symasha...@gmail.com wrote

[gmx-users] GPU build error

Hi, I am trying to build with GPU acceleration, and I get the following build error. However, if set GMX_GPU=OFF and keep MPI=ON it compiles. Could anyone please suggest how to resolve the issue? Thanks, Sikandar /home/projects/cuda/6.0.37/bin/nvcc