[gmx-users] error during solvation of system

Dear all I am doing simulation of membrane protei in lipid bilayer after making complex of protein and lipid bilayer I was going to step genbox to solvate the system but when I was doing this the one error came like this- Program genbox, VERSION 4.0.3 Source code file:

Re: [gmx-users] error during solvation of system

nitu sharma wrote: Dear all I am doing simulation of membrane protei in lipid bilayer after making complex of protein and lipid bilayer I was going to step genbox to solvate the system but when I was doing this the one error came like this- Program genbox, VERSION 4.0.3

[gmx-users] Hi .. Gr8 offer

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[gmx-users] gmx4.0.3: simulations do not run on 16 processors but do run on 10

Dear all, I am trying to run some simulations on our institutional cluster using gmx4.0.3. My systems are membrane proteins in lipid bilayers although for the error I am getting I do not think this is important (this is just my impression because a couple of months ago I got something similar with

Re: [gmx-users] Re: Replacement for G43b1 force field?

Anirban Ghosh wrote: Thanks a lot Justin for the reply. I have already seen that post. But the problem is that there is no clear answer in it. Hess says that there NO G43b1 force-field now in GROMACS and G43b1 was just a modified version of G43a1 but with no residue charges. So this means

[gmx-users] find with which mpi library /environment gromacs was compiled

Hello,I have a cluster with gromacs compiled. I would like to know which parallel environment I'm using. The version of operating system I use is centos version 5.1. When I open qmon and see the parallel environments that I have at my disposal I can see:lammpimpichorteI do know every command

Re: [gmx-users] find with which mpi library /environment gromacs was compiled

Claus Valka wrote: Hello, I have a cluster with gromacs compiled. I would like to know which parallel environment I'm using. The version of operating system I use is centos version 5.1. When I open qmon and see the parallel environments that I have at my disposal I can see: lam mpi mpich

Re: [gmx-users] gmx4.0.3: simulations do not run on 16 processors but do run on 10

Ángel Piñeiro wrote: Dear all, I am trying to run some simulations on our institutional cluster using gmx4.0.3. My systems are membrane proteins in lipid bilayers although for the error I am getting I do not think this is important (this is just my impression because a couple of months ago I got

Re: [gmx-users] Error by pdb2gmx

Dear Mark: This error is being provoked at the top of the .rtp file when a line with something like [header] is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that. Would you mind telling me how to do that in detail? I tried the following and it doesn't work.

Re: [gmx-users] Error by pdb2gmx

Yanmei Song wrote: Dear Mark: This error is being provoked at the top of the .rtp file when a line with something like [header] is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that. Would you mind telling me how to do that in detail? On a command line, diff

[gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after

Hi, all There are some things confusing and resulting in error when I run mdrun for energy minization and md. I use Gromacs 4.0.4 to simulate electroosmotic flow in slab geometry with only 2 dimensional periodic boundary (x and y), the system is aqueous solution with some ions, eg. CL- and Na+,

[gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?

Hello, I am facing a problem with g_angle. I want to analyse some dihedrals. When calculating the autocorrelation function, g_angle crashes if I want to use a Legendre polynomial for the ACF. Can I somehow handle this problem? The command lines are below together with the error message. I am