Re: [gmx-users] bilayer DMPC

Search the list archive for rvdw with lipids, membranes or similar keywords. Also look the rvdw values used in published work. There have been discussions about balancing attractive and repulsive forces and the cutoff values can have a strong influence on area. And as others pointed, compare

Re: [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?

Dear Maria, I am not sure but something you should look further is the rotation around your P3-O2 bond (which is P8-O7 in Tieleman's topology). It is described by the first two lines of your dihedral section topology: 1 2 3 6 10.0 1.05 3 1 2 3 6

Re: [gmx-users] Re: installation problem for MAC OS

Hello, I just encounter the same "bad pc-rel vanilla relocation length collect2" error on an Intel Mac running the Server version of Leopard and taking the CVS release as proposed by Erik fixed also the problem. Many thanks! Ioannis Le 8 févr. 08 à 11:17, Erik Lindahl a écrit : Hi Warner,

Re: [gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo

Le 29 mai 06 à 20:46, David van der Spoel a écrit : Yiannis wrote: Hello, Has anybody tried to use gromacs in parallel with the Intel Core Duo macintoshes? I installed gromacs and lam on some iMac with intel core duo 2x1.83GHz running the latest OSX with all updates. I have everything

[gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo

Hello, Has anybody tried to use gromacs in parallel with the Intel Core Duo macintoshes? I installed gromacs and lam on some iMac with intel core duo 2x1.83GHz running the latest OSX with all updates. I have everything working OK but the scaling is very inefficient. Here are the results of t

Re: [gmx-users] problem going from cut-off to pme

Le 8 mars 06 à 22:22, Mark Abraham a écrit : Yiannis wrote: Le 8 mars 06 à 20:35, Mark Abraham a écrit : Yiannis wrote: Well, my initial guess was something wrong with the structure. But the same gro file gives a correct minimisation with cut-off. So I tried a 0 step minimisation to see

Re: [gmx-users] problem going from cut-off to pme

Le 8 mars 06 à 20:35, Mark Abraham a écrit : Yiannis wrote: Well, my initial guess was something wrong with the structure. But the same gro file gives a correct minimisation with cut-off. So I tried a 0 step minimisation to see which component is different. Here it is: ==> cutoff.

Re: [gmx-users] problem going from cut-off to pme

o coulombtype = pme I don't understand why the Coulomb SR is different and even more why it is illogical. Could it be pme parameters? I keep the defaults (pme=4 or 8 does change a little the reciprocal component but not the SR). Yiannis Le 8 mars 06 à 07:14, Mark Abraham a éc

[gmx-users] problem going from cut-off to pme

Hello, I have a strange problem with a 100 molecule system where I used cut- off electrostatics and I want to use pme from now. After md with Coulomb cut-off, I minimised with steep (and the same Coulomb cut-off) and it ends OK: Step= 395, Dmax= 1.7e-06 nm, Epot= -5.04260e+04 Fmax= 1.15989