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

이 선주 wrote: > 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

[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

Re: [gmx-users] do_dssp

Tsjerk Wassenaar wrote: Hi Gurpreet, The common message is "don't worry, mdrun doesn't write broken molecules". So you're secondary structure will not be affected by periodic boundary conditions. Cheers, Tsjerk On 12/21/06, singh <[EMAIL PROTECTED]> wrote: But there could be a problem for b

Re: [gmx-users] do_dssp

Hi Gurpreet, The common message is "don't worry, mdrun doesn't write broken molecules". So you're secondary structure will not be affected by periodic boundary conditions. Cheers, Tsjerk On 12/21/06, singh <[EMAIL PROTECTED]> wrote: Dear Gromacs users, I have simulated 12 peptide f

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

Am Donnerstag, 21. Dezember 2006 08:41 schrieb Seaclear Theory: Hi Ocean, > When I run mdrun, I got message that lamboot is not start. Then I start the > lamboot and try to run mdrun witn "-np 4 -v N 4" (gromacs user guide try mpirun -np 4 mdrun -np4 -bla -blubb This should be necessary on mos

[gmx-users] do_dssp

Dear Gromacs users, I have simulated 12 peptide fragments in a cubic box and I want to use do_dssp for secondary structure analysis but I am not sure whether Periodic boundary conditions will be taken in account during assignment (particularly for assigning betasheets). Regards, Gurp

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

Seaclear Theory wrote: I do not understand why you are so upset. Are you the author of the user manual :-) Any way, let's go back for the issue, not person. I'm not upset - I'm just communicating directly :-) I do get a little irritated when someone wanting help doesn't describe their probl

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

Will work on it. Thanks. Ocean On 12/21/06, David van der Spoel <[EMAIL PROTECTED]> wrote: Seaclear Theory wrote: > I believed the case that single machine with multiple processors (like > Dell server with 2 due core CPUs) should be very popular for end user. > Because not everyone can offer a

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

Seaclear Theory wrote: I believed the case that single machine with multiple processors (like Dell server with 2 due core CPUs) should be very popular for end user. Because not everyone can offer a 32 nodes cluster or has access to supercomputer center. Could we have detail tutorial for "run

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

I believed the case that single machine with multiple processors (like Dell server with 2 due core CPUs) should be very popular for end user. Because not everyone can offer a 32 nodes cluster or has access to supercomputer center. Could we have detail tutorial for "run gromacs on single machine

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

Thanks for your help very much. Best, Ocean On 12/21/06, Yang Ye <[EMAIL PROTECTED]> wrote: normally we use following commands when compiling gromacs ./configure ... --program_suffix=_mpi --enable-mpi ... So we will have mdrun_mpi in the end. The usage of mdrun_mpi is the same as mdrun but

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

Yang Ye wrote: normally we use following commands when compiling gromacs ./configure ... --program_suffix=_mpi --enable-mpi ... So we will have mdrun_mpi in the end. The usage of mdrun_mpi is the same as mdrun but -np, -replex and other switches are activated. That statement on the user manu

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

normally we use following commands when compiling gromacs ./configure ... --program_suffix=_mpi --enable-mpi ... So we will have mdrun_mpi in the end. The usage of mdrun_mpi is the same as mdrun but -np, -replex and other switches are activated. That statement on the user manual is to clarify

Re: [gmx-users] run gromacs on a single machine with mutiple CPUs

On 12/20/06, Mark Abraham <[EMAIL PROTECTED]> wrote: Seaclear Theory wrote: > > > On 12/20/06, *Mark Abraham* <[EMAIL PROTECTED] > > wrote: > > Seaclear Theory wrote: > > Hi! All, > > > > I have a linux server with 4 CPUs. How can I run gromacs on all