Re: [gmx-users] gromacs parallel doesn't work

Beniamino Sciacca wrote: I never used mprun -np 2, and I had not problem. Before I didn't use "mprun -np 2", now I don't use "mprun -np 2" but simulation time now is twice. It has changed from a day to the other. However I've just tried, like you suggested, to use " -np 2" (in grompp and in md

Re: [gmx-users] gromacs parallel doesn't work

Beniamino Sciacca wrote: I don't understand what you talking about... I didn't write any hostfile I'm not in a cluster. I only use my notebook with the two cores. In fact I type "lamboot" without -v... Beniamino Mark Abraham ha scritto: Did your default LAM hostfile configuration (or

[gmx-users] Conformation free energy

Hello, I am studying a protein that has an amino acid modeled as a two-state rotamer in the crystal structure. I would like to quantify the probability of each conformation, so I thought of doing a FEP calculation. As I haven't seen much about this in the mailing lists, save for a D- L- amino ac

Re: [gmx-users] gromacs parallel doesn't work

Yang Ye wrote: First, make sure that you used mdrun -np 2. Second, check your energy profile. Is your laptop running in top speed? or does it have sleep time? mpirun -c 2 mdrun Yang Ye Beniamino Sciacca wrote: I don't understand what you talking about... I didn't write any hostfile I'

Re: [gmx-users] gromacs parallel doesn't work

I never used mprun -np 2, and I had not problem. Before I didn't use "mprun -np 2", now I don't use "mprun -np 2" but simulation time now is twice. It has changed from a day to the other.However I've just tried, like you suggested,  to use " -np 2" (in grompp and in mdrun) but I obtain an error: -

Re: [gmx-users] gromacs parallel doesn't work

First, make sure that you used mdrun -np 2. Second, check your energy profile. Is your laptop running in top speed? or does it have sleep time? Yang Ye Beniamino Sciacca wrote: I don't understand what you talking about... I didn't write any hostfile I'm not in a cluster. I only use my no

Re: [gmx-users] gromacs parallel doesn't work

I don't understand what you talking about... I didn't write any hostfile I'm not in a cluster. I only use my notebook with the two cores. In fact I type "lamboot" without -v... Beniamino Mark Abraham ha scritto: Did your default LAM hostfile configuration (or whatever it is) change fr

gmx-users@gromacs.org

SUN, Jian wrote: Dear all, I am running simulated annealing for a protein in water and found something strange: 1. the poteintial energy keep on rising while the system is cooling down conservation of energy? 2. several LINCS WARNINGs are given (I have posted the question but no reply till

gmx-users@gromacs.org

Dear all, I am running simulated annealing for a protein in water and found something strange: 1. the poteintial energy keep on rising while the system is cooling down 2. several LINCS WARNINGs are given (I have posted the question but no reply till now) and then the energies become "nan" Who can

Re: [gmx-users] editconf

Beniamino Sciacca wrote: Hi! I've another question: I've a DNA molecule, and I make a rigid traslation of the entire system. If I try to display the new molecule with VMD, it doesn't display anything! Instead if I run editconf on the new traslated molecule VMD works and I see the molecule, but u

Re: [gmx-users] gromacs parallel doesn't work

Did your default LAM hostfile configuration (or whatever it is) change from 2 processors to one? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the

[gmx-users] editconf

Hi! I've another question: I've a DNA molecule, and I make a rigid traslation of the entire system. If I try to display the new molecule with VMD, it doesn't display anything! Instead if I run editconf on the new traslated molecule VMD works and I see the molecule, but using editconf the position

[gmx-users] gromacs parallel doesn't work

Hi gmx-user! I've a great problem: two months ago I installed LAM on my centrino duo, debian -kernel 2.6. Later I compiled gromacs enabling mpi, and everything was working well until four days ago. Now the simulation time is increased like if there is only one processor (it takes twice time than