[gmx-users] limit of number of processors ??

Hello All, I have been doing membranes simulations using the computer nodes in UTEXAS supercomputing center. Each board contains two Xeon Intel Duo-Core 64-bit processors (4 cores in all) and nodes are interconnected with InfiniBand technology. The performance is great. However, I have got w

[gmx-users] g_potential: better precision

Dear All, I am trying to calculate membrane potential from the charge density. I have calculated membrane potential from the charge density profile obtained from g_potential function. But I've got unmatched potential between block-averaged(10 ns *6) potential and the potential from the whole

[gmx-users] Analysis for the big systems containing more than 100, 000 atoms

Dear Users I am recently trying to analyze a double bilayer system, which contains more than 100,000 atoms. While I was caculating g_potential, I found out that the index number was redundant, and presumably becuase of that, the potential profile was really weird. Does anyone have this proble

[gmx-users] Re: constrained minimization (David van der Spoel)

> Dear All > > I just saw from the mailing list that David answered that the restrained > minimization can be done and it is different from the constrained > minimization. For the torsional parameter optimization, I think I need > to run minimization after constraining torsion angles. Does anyo

[gmx-users] constrained minimization

Dear All I just saw from the mailing list that David answered that the restrained minimization can be done and it is different from the constrained minimization. For the torsional parameter optimization, I think I need to run minimization after constraining torsion angles. Does anyone know t

[gmx-users] Converting OPLS_AA to gromacs

Dear Gromacs people Recently I am trying to parameterize small molecules. Unfortunately the gromacs force field does not contain atom types necessary. So I am thinking about adopting atom types from OPLS_AA force field. It will be grateful if anyone can tell me guide lines for the converting.

[gmx-users] Supradiffusivity

Hello Users I have seen that it is needed to define three separate groups for center-of-mass motion removal: water and a separate group for each lipid layer in order to remove supradiffusivity of the two leaflets. Can anyone tell me whether my settings are correct? --

[gmx-users] off-diagonal of the tensor for pressure coupling should be zero??

Dear Gromacs people I am trying to run NPT simulation on a bilayer and want to know right setup to use anisotropic pressure coupling. I have seen two different cases of reference pressure. Some people use 1 atm for off-diagonals (xy, yz, zx directions) but other use 0 atm. From Erik's answer