[gmx-users] Conserved quantity in NPT simulations

Hi, I am wondering how to test the conserved quantity in an NPT simulation fron the ener.edr file. As you well know for npt with a Nose-Hoover thermostat and a Parrinello-Rahman barostat, the conserved quantity is not just K+P, but contains additional terms function of the additional npt

[gmx-users] installing on macbook

hi.. i have problem in installing gromacs in my macbook pro ( personal pc) .. can anyone help me with this?? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] installing on macbook

On 10/24/14 6:32 AM, Suraya Abdul Sani wrote: hi.. i have problem in installing gromacs in my macbook pro ( personal pc) .. can anyone help me with this?? Not unless you tell us exactly what you're doing - exact cmake command, exact error messages, etc. In general, follow

Re: [gmx-users] Conserved quantity in NPT simulations

Those conserved quantities are indeed included in the reported information. For thermostats/barostats where there is such a quantity, it's included in the .edr file. On Fri, Oct 24, 2014 at 4:23 AM, Paolo Franz paolo.fr...@gmail.com wrote: Hi, I am wondering how to test the conserved quantity

Re: [gmx-users] installing on macbook

Hi Suraya. I have succesfully installed Gromacs 4.5, 4.6, and 5.0 on my macbook pro running OS X Mavericks, even with CUDA support. I am not using apple compiler because apple compiler in Mavericks (clang 3.4) doesn't support OpenMP, that will cause many errors when compiling gromacs (my

Re: [gmx-users] error in the middle of running mdrun_mpi

Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages

Re: [gmx-users] error in the middle of running mdrun_mpi

On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated

[gmx-users] use of Walls in Martini simulations

Hi, I would like to post a question about simulating with Walls in gromacs and using the Martini force field. The question is very simple. I am trying to simulate a simple box of water molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling and no pressure bath. I am

Re: [gmx-users] numerical matrix from xpm file

Hi Tsjerk, This is a very useful script. Just found a small bug that is only noticeable if one is using higher -nlevels for the .xpm construction (in g_rms, for example) z = [colors[j[k:k+nb]] for k in range(0,nx,nb)] should be z = [colors[j[k:k+nb]] for k in range(0,nx*nb,nb)] instead. At least

Re: [gmx-users] use of Walls in Martini simulations

What about electrostatics? Ewald summation is probably the culprit here. On Oct 24, 2014 12:05 PM, Ramon Reigada reig...@ub.edu wrote: Hi, I would like to post a question about simulating with Walls in gromacs and using the Martini force field. The question is very simple. I am trying to

Re: [gmx-users] Multiple writing to same trajectory issue

Just one more question on that topic: according to the Hoempage (http://www.gromacs.org/Documentation/How-tos/Doing_Restarts - After a crash), it used to be possible to resume a crashed run by employing tpbconv and supplying the trr file. As I did not save my cpt-files, would that still be an

[gmx-users] Question about Walls

Hi, I would like to post a question about simulating with Walls in gromacs. The question is very simple. I am trying to simulate a simple box of water molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling and no pressure bath. I am trying: pbc=xy nwall =2

[gmx-users] Cannot combine residue position based cog selection with index output for g_select

Hi, I have a system consists of a box of water and a monolayer of polymer in the center. I am trying to extract solvent molecules that have z coordinates greater than 5 nm using g_select and output an index file. Basically I want to separate my system into two portions: a box of waters above the