Re: [gmx-users] Hamiltonian replica exchange not working in 4.6

Hi, Sanku- The way to invoke Hamiltonian replica exchange has changed to be a bit more flexible. We should go back and make sure that this legacy way is supported (I thought this invocation was supported, but apparently it isn't), but what you should be able to do to get it working quickly is inc

RE: [gmx-users] set charge as 0 in gromacs code

Hello Mark, Thanks for your reply!!! Not self energy term. For my research reason, I would like to turn off the long-ranged electrostatics between SOL and CL. That is to say, SOL and CL only interacts with erfc(eta*r)/r potential, without reciprocal electrostatics parts. I use PME in the mdp

Re: [gmx-users] set charge as 0 in gromacs code

Ewald self energy, perhaps? Mark On Wed, Aug 7, 2013 at 1:16 AM, Shi, Yu (shiy4) wrote: > Hello everyone, > > My system is 512 waters and 1 ion CL-. Now I would like to change the CL > charge as 0 in the gromacs code for the short non-bonded interaction. While > for the long-range electrosta

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

That all looks fine so far. The core file processor won't help unless you've compiled with -g. Hopefully cmake -DCMAKE_BUILD_TYPE=Debug will do that, but I haven't actually checked that really works. If not, you might have to hack cmake/Platform/BlueGeneP-static-XL-C.cmake. Anyway, if you can comp

[gmx-users] set charge as 0 in gromacs code

Hello everyone, My system is 512 waters and 1 ion CL-. Now I would like to change the CL charge as 0 in the gromacs code for the short non-bonded interaction. While for the long-range electrostatics (pme) the CL is -1. My gromacs version is 4.6.2, which automatically starts 8 threads to com

[gmx-users] Hamiltonian replica exchange not working in 4.6

Dear Gromacs user,   I am not sure whether this is any potential bug. But I found that in gromacs4.6.3, hamiltonian replica exchange simulation is not working. The SAME simulation works perfectly fine in gromacs 4.5.4 But, when I try to run the simulation using gromacs4.6.3, I get following error:

Re: [gmx-users] g_angle bin centers

On 8/6/13 3:38 PM, Brandon Wiebe wrote: Hello, I have a question about the way g_angle centers the bins when it calculates angle/dihedral distributions. I dug around a bit in the source code and found a comment saying that the bins are centered at start+n*binwidth if you have integer bins,

[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

Dear GMX-users, I need some assistance running Gromacs 4.6.3 on a Blue Gene/P. Although I have a background in Chemistry, I'm an experienced professional HPC admin who's relatively new to supporting Blue Genes and Gromacs. My first Gromacs user is having trouble running Gromacs on our BG/P. H

[gmx-users] g_angle bin centers

Hello, I have a question about the way g_angle centers the bins when it calculates angle/dihedral distributions. I dug around a bit in the source code and found a comment saying that the bins are centered at start+n*binwidth if you have integer bins, else they are centered at start+(n+0.5)*bin

Re: [gmx-users] Re: starting temperature equilibration phase

On 8/6/13 2:45 PM, ypca wrote: Thank you for the help! I can completely understand you, but what about the simulated annealing, isn't it automatically for all systems? No. If you want to perform simulated annealing, use simulated annealing options (see the manual). Why the increase of te

[gmx-users] Re: starting temperature equilibration phase

Thank you for the help! I can completely understand you, but what about the simulated annealing, isn't it automatically for all systems? Why the increase of temperature is so fast, like in lysozyme tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.h

Re: [gmx-users] starting temperature equilibration phase

On 8/6/13 1:49 PM, ypca wrote: Hello, I'm studying a protein in water at 348 K. In the equilibration phase (nvt, 1 ns) the temperature starts at about 348 K, and i can't see the slowly increase of the temperature. I can't understand why the temperature is so high at the beginning. Could anyone

[gmx-users] starting temperature equilibration phase

Hello, I'm studying a protein in water at 348 K. In the equilibration phase (nvt, 1 ns) the temperature starts at about 348 K, and i can't see the slowly increase of the temperature. I can't understand why the temperature is so high at the beginning. Could anyone help me? Thanks. -- View this

[gmx-users] Re: Gromacs 4.6.3 installation Issue with Intel & CUDA

I have just successfully installed 4.6.3 using Intel compilers this morning with the following: Intel 12.1.3 cuda 5.0.35 openmpi 1.6.2 cmake 2.8.10.2 FFTW 3.3.3 I did not use gcc at all. (intel/12.1.3/icc/bin/icc for CUDA_HOST_COMPILER) Hope it helps, Brad -- View this message in context: h

[gmx-users] Free Energy Ion Pair Decoupling

Dear Gromacs users, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interf

Re: [gmx-users] The sum of the two largest charge group radii ..is larger than rlist

Ok Thank you. Regards Kavya On Tue, Aug 6, 2013 at 3:02 PM, Justin Lemkul wrote: > > > On 8/6/13 2:35 AM, Kavyashree M wrote: > >> Dear users, >> >> >> After EM step while running NVT I gor a warning saying - >> >> Largest charge group radii for Van der Waals: 3.798, 1.293 nm >> Largest charge

Re: [gmx-users] The sum of the two largest charge group radii ..is larger than rlist

On 8/6/13 2:35 AM, Kavyashree M wrote: Dear users, After EM step while running NVT I gor a warning saying - Largest charge group radii for Van der Waals: 3.798, 1.293 nm Largest charge group radii for Coulomb: 7.565, 3.798 nm The sum of the two largest charge group radii (11.362685) is