Re: [gmx-users] Parellel Gromacs

I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename did you try the following mpirun -np 2 mdrun_mpi -deffnm filename XAvier Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

Re: [gmx-users] Calculation of the bending modulus (Kc) of bilayer using spectral intensity.

Hwankyu Lee wrote: Dear gmx-users, I'm trying to measure the bending modulus (Kc) of lipid bilayer with different sizes. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q, but couldn't understand details. I wonder if I can hear more detai

Re: [gmx-users] Do you need to have the parameters numbered in order?

Arthur Roberts wrote: To Whom It May Concern: Do you need to have the parameters numbered in order? No. Reading chapter five would tell you this. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Calculation of the bending modulus (Kc) of bilayer using spectral intensity.

Dear gmx-users, I'm trying to measure the bending modulus (Kc) of lipid bilayer with different sizes. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q, but couldn't understand details. I wonder if I can hear more details and how to do th

Re: [gmx-users] Parellel Gromacs

you should use the mdrun_mpi probably XAvier Hi, I am not the one who built it, but it is MPI supported. Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromac

Re: [gmx-users] Parellel Gromacs

Hi, I am not the one who built it, but it is MPI supported. > Have your built the GROMACS with MPI-support? > > Regards, > Yang Ye > > On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: >> Dear Gromacs users, >> >> I am trying to do Parellel calculations using Gromacs on a Rocks >> cluster >> that

Re: [gmx-users] Parellel Gromacs

Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION

[gmx-users] Parellel Gromacs

Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was mad

[gmx-users] x2top & GMXLIB

I have been having an odd problem that I can not seem to figure out. When running x2top in a folder within a folder in my home dir it works fine but when I go one folder deeper its gives the following error: ## Program x2top, VERSION 3.3.1 Source code file: futil

[gmx-users] Do you need to have the parameters numbered in order?

To Whom It May Concern: Do you need to have the parameters numbered in order? For example: [ bonds ] ; aiaj functc0c1 c2c3 1 2 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.41611228368 Angstroms 1 6 2 gb_16 ; CR

Re: [gmx-users] Chitosan topology

Hi, Please describe clearly your "poor results". Regards, Yang Ye On 7/31/2007 10:55 PM, Antonello wrote: Dear gromacs users, i apply to your kind attention to know if someone have already parametrized the chitosan structure. I am trying to do it but with poor results. Can you help me?

[gmx-users] Chitosan topology

Dear gromacs users, i apply to your kind attention to know if someone have already parametrized the chitosan structure. I am trying to do it but with poor results. Can you help me? Thanking in advance Dipartimento di Medicina Sperimentale Universita' degli Studi di Parma __

Re: [gmx-users] GRomacs 3.3.1 parallel run

Hi, its a problem of your cluster configuration, ask your local sysadmin. On Tuesday, 31. July 2007 15:43, fabio tombolato wrote: > Good morning, I started using Gromacs only few months ago doing MD on > proteins in membranes. > I' m using GRomacs 3.3.1 in parallel but I have some problems. I'm >

[gmx-users] GRomacs 3.3.1 parallel run

Good morning, I started using Gromacs only few months ago doing MD on proteins in membranes. I' m using GRomacs 3.3.1 in parallel but I have some problems. I'm doing my simulations on a 70 nodes cluster using 4 nodes (16 processors). the system uses PBS torque and SCALIMPI libraries. When I run my