Re: [gmx-users] GROMACS 4.6 with GPU acceleration (double

ail >On 2013-04-09 18:06, Mikhail Stukan wrote: >> Dear experts, >> >> I have the following question. I am trying to compile GROMACS 4.6.1 with GPU >> acceleration and have the following diagnostics: >> >> # cmake .. -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=O

[gmx-users] GROMACS 4.6 with GPU acceleration (double presion)

Dear experts, I have the following question. I am trying to compile GROMACS 4.6.1 with GPU acceleration and have the following diagnostics: # cmake .. -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DCUDA_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE

[gmx-users] Spherical constraint (spherical force)

t how this approach can be realized in GROMACS? I looked through the manual, but did not find clear answer how to implement such a force. Thank you very much in advance. Mikhail ===== Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhah

[gmx-users] Viscosity measurements

= 0.1 Pcoupl = no gen_vel = no gen_temp = 300 gen_seed = 473529 = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011

[gmx-users] Velocity and temperature profiles

= Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 6182 Fax:+966 3 330 0845 mstu...@slb.com<mailto:mstu...@slb.com> -- gmx

[gmx-users] Velocity distribution (a bug?)

Dear gmx-users, I have performed further investigation on the subject of the velocity distribution http://lists.gromacs.org/pipermail/gmx-users/2011-April/060316.html and what I found looks like a sort of a bug to me. Namely, the velocity distribution profiles are different if I simulate a

[gmx-users] Velocity distribution

Dear gmx-users, I am currently trying to simulate a thermalized wall of coarse-grained particles. I model the wall in the framework of the bead on spring approach. The wall molecules are defined as dimers : [ moleculetype ] ; molname nrexcl ROCK1 [ atoms ] ;id type

[gmx-users] Position restraints

particles will be written out at the end of the run? The initial ones ("reference positions") or the instantaneous position of these particle at the end of the run? Many thanks in advance, Mikhail ========= Dr Mikhail Stukan Schlumberger Dhahran Carbo

[gmx-users] Re: Polarizable halide (Iodide)

David, What should not be working in the current version? Do you mean that any polarizable model (water for example) can run on a single processor only? I am currently using the model by Roux et al. for NaCl solution in SWM4-NDP model and everything seems to be working fine. I also had some prob

[gmx-users] Re: g_energy: Energy names magic number mismatch

Justin, Thanks a lot. Concatenation seems to be the only solution, but it works fine. It look like there are some problems with the appending routine on BlueGene. Mikhail > Dear Justin and Berk, > > Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version > doesn't solve the p

RE: Re: [gmx-users] g_energy: Energy names magic number mismatch

Dear Justin and Berk, Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version doesn't solve the problem, diagnostic is still the same: == Program g_energy_d, VERSION 4.5.3 Source code file: ../../../src/gmxlib/enxio.c, line: 422 Fatal error: Ener

[gmx-users] g_energy: Energy names magic number mismatch

Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type= bluegene # @ output

[gmx-users] v-rescale and conserved energy

Dear gromacs users, I am running NVT simulations for polarizable (shell particle) water model (GROMACS version 4.5.1 and 4.5.3 (issue is same in both)) using v-rescale thermostat. While temperature, potential, kinetic and total energies behave quite well I am failing to obtain constant values

[gmx-users] g_h2order for 5 sites water

Dear gmx-users, I have the following problem with g_h2order tool (4.0.7 and 4.5.1 versions). It works perfectly fine when I apply it to a box of SPC/E water, but I have something really strange if I try to apply it to SW or SWM4-NDP water models (both are 5 sited models). In my index file I ha

Re: RE: [gmx-users] Dispersion correction in a heterogeneous

Berk, Thank you very much for the answer. It was not clear from my post (sorry for that) but my main concern was indeed related to the inhomogeneity near the surfaces. I am not targeting complete quantitative agreement, but I would like to be save from "hidden" undesired qualitative effects. As

[gmx-users] Dispersion correction in a heterogeneous system

= Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966 3 330 0845 mstu...@slb.com<mailto:mstu...@slb.com> -- gmx

[gmx-users] Problem with pressure form g_energy

occur. Thank you very much in advance, Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966

[gmx-users] SWM4-NDP water model in GROMACS

; random seed = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966 3 330 0845 mstu...@slb.com

[gmx-users] Different impacts in the pressure

, Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966 3 330 0845 mstu...@slb.com<mailto:m

[gmx-users] fcstep value for shell particles

mean from the computational point of view. Let say, what should be fcstep value if one would like to run SW water model by van Maaren and van der Spoel? Many thanks in advance, Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research C