[gmx-users] Re: Potential energy from a previous configuration mismatch

Yes, that seems to be the problem. I minimized the configuration using Conjugated Gradient and everything looks right now. Thank you again! -- View this message in context: http://gromacs.5086.n6.nabble.com/Potential-energy-from-a-previous-configuration-mismatch-tp5003352p5003432.html Sent

Re: [gmx-users] Build on OSX with 4.6beta1

Hi, I think this happens either because you have cmake 2.8.10 and the host-compiler gets double-set or because something gets messed up when you use clang/clang++ with gcc as the CUDA host-compiler. Could you provide the exact error output you are getting as well as cmake invocation? As I don't

Re: [gmx-users] Build on OSX with 4.6beta1

the most efficient way is just give up a macOS and switch to a more reasonable OS like Linux. macOS is definitely a pain in the neck , and it is completely nightmare to use it for computational work. On 12/03/2012 04:10 PM, Szilárd Páll wrote: On Fri, Nov 30, 2012 at 11:01 AM, Carlo

Re: [gmx-users] Build on OSX with 4.6beta1

On 12/3/12 10:24 AM, Albert wrote: the most efficient way is just give up a macOS and switch to a more reasonable OS like Linux. macOS is definitely a pain in the neck , and it is completely nightmare to use it for computational work. I think every OS has something to complain about,

Re: [gmx-users] Build on OSX with 4.6beta1

On 12/03/2012 04:40 PM, Justin Lemkul wrote: I think every OS has something to complain about, though Linux seems to be the most friendly. Yes, Mac has its quirks and annoyances (as does Windows, which is becoming more and more common in the scientific realm), but I would disagree that it's a

Re: [gmx-users] Build on OSX with 4.6beta1

On 12/3/12 10:48 AM, Albert wrote: On 12/03/2012 04:40 PM, Justin Lemkul wrote: I think every OS has something to complain about, though Linux seems to be the most friendly. Yes, Mac has its quirks and annoyances (as does Windows, which is becoming more and more common in the scientific

Re: [gmx-users] metal_ligand complex

On 12/3/12 12:09 PM, tarak karmakar wrote: Dear All, In my system, I want to see the binding of a ligand, composed of a divalent metal and 6 ligands, to a protein. I am not sure that movement of this type of complex ( ligand) towards the protein active site cavity can be feasible or not. If

Re: [gmx-users] Can i construct a solid wall in gromacs?

On 12/3/12 12:58 PM, Ali Alizadeh wrote: Dear All users Can i construct a solid wall in gromacs? Gromacs does not have extensive tools for building configurations, but genconf is able to replicate coordinates passed to it to create grids, which may be useful. -Justin --

[gmx-users] Installing 4.6 beta1

Hey Dear, when I try to install the GROMACS-4.6-beta1 version I get an error which I can not pin down when do make. My system: CPU: i7 GPU: NVIDIA GTX670 gcc: Debian 4.4.5-8 CUDA: 4.2 fft3w: 3.3.2 including sse2 Debian Linux 64-bit First I do: cmake ../

Re: [gmx-users] Build on OSX with 4.6beta1

Hi, Preferably we should avoid starting an OS flame-war here. However, before this thread turns into an ode to Apple, I have to say: Mac OS X is/can be a pain both for development and computational use. As long as you use it to code for iPhone or write some Mac app in Xcode, it's probably

Re: [gmx-users] Installing 4.6 beta1

Looks like a compiler bug to me, and google agrees http://gcc.gnu.org/bugzilla/show_bug.cgi?id=47318. Even if there were not this bug, we would strongly encourage you to get the better performance available from more recent versions of gcc. I was about to suggest 4.6 or newer, but the above URL

[gmx-users] Re: gmx-users Digest, Vol 104, Issue 7

Dear Szilárd, My cmake version in the 2.8.9. The error is Linking C shared library libgmx.dylib Undefined symbols for architecture x86_64: std::terminate(), referenced from: do_memtest(unsigned int, int, int) in libgpu_utils.a(gpu_utils_generated_gpu_utils.cu.o)

Re: [gmx-users] Installing 4.6 beta1

Hi, a small addition to Mark's answer. If you want/need to use an older gcc version 4.4.6 and 4.5.3 have the necessary fix too. Also you can disable AVX with cmake -DGMX_CPU_ACCELERATION=SSE4.1 . But you will get somewhat lower performance (AFAIK only 10% with group kernels but more with verlet

Re: [gmx-users] metal_ligand complex

Thanks Justin Yah! We can run steered MD or Umbrella Pulling ( sampling) for this purpose. But one thing I am wondering that how to move the entire complex. In my model there are no covalent bond ( bonding info) between the metal and ligands. So how to select a particular point in the complex to

[gmx-users] g_rms alignment question

Dear gromacs users, I have a trajectory of 500-atom system and would like to obtain RMSD of all atoms but only aligned to residue 1-400 of a reference structure. Is there any way to do this? Thank you so much! Regards, Jia -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: Can i construct a solid wall in gromacs?

I once constructed a solid hydrophilic wall by applying large constraints on an equilibrated slab of spce water. Just construct a simulation box of the size of the wall needed (don't make it too thin), equilibrate it, use genrestr in all 3 dimensions to construct a restraints file, and then