Re: [gmx-users] Error in BlueGene

Hello, before submitting to Bluegene, I always test the system in my local 8 core cpu, and if it works, it will also work in Bluegene, as long as I balance the domain decomposition for the larger number of cores. If your system insists in exploding, even after energy minimization, you could try to

Re: [gmx-users] g_bar for larger systems (protein-protein interaction)

On Mon, 25 Feb 2013 15:55:05 -0500, Michael Shirts wrote > My personal opinion is that for large protein-protein calculations, > the free energy should be computed through potential of mean force > calculations, NOT alchemical methods, using the endpoints (properly > corrected) to determine the fre

Re: [gmx-users] simulation box

noob noob wrote: Dear all, I am new about MD simulation and I have some questions about the box size. I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 nm ) but now I change to a bigger molecules and increase the number of molecules. So,the new system cannot fix into t

Re: [gmx-users] box size

noob noob wrote: Dear all, I am new about MD simulation and I have some questions about the box size. I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 nm ) but now I change to a bigger molecules and increase the number of molecules. So,the new system cannot fix into t

[gmx-users] Concerning DSSP

Hello everyone. I'm new to this list and first of all I'd like to salute all the members and crew. I'm having a little problem with permissions with the DSSP program, should anybody help me I'd be glad. I've already read the forum but couldn't find an answer. I'm running GROMACS in two compu

Re: [gmx-users] Concerning DSSP

Thanks David, Well, dsspcmbi is working fine without gromacs. So maybe the problem lies in the integration dssp-gromacs, with some user restrictions, isn't? -- ___ Ricardo Oliveira dos Santos Soares Post-graduation Student in Biological

Re: [gmx-users] Concerning DSSP

Yes, I have permission to both view and modify content. I even run the do_dssp command with the sudo (root user) option enabled. I think that the problem may then be related to sh: "sh: /path/to/dssp: Permission denied" I'll try to change its permissions and post another message later with th

Re: [gmx-users] Concerning DSSP

Hello Justin, Not a naive question at all. The actual path to DSSP on my machine is /usr/bin/dssp, I just wrote /path/to/dssp to generalize my explanation. But thanks for the tip! -- ___ Ricardo Oliveira dos Santos Soares Post-graduation

[gmx-users] Computational efficiency

Hello everyone, I have 3 available computers for my simulations; two of them are dual core. Which is better for me: run one simulation each independently or parallelize them all? Thanks! Ricardo. -- ___ Ricardo Oliveira dos Santos Soa

Re: [gmx-users] Computational efficiency

Diego Enry wrote: On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote: Hello everyone, I have 3 available computers for my simulations; two of them are dual core. Which is better for me: run one simulation each independently or parallelize th

[gmx-users] Gromacs setup on dual core machine

Hi everybody, I think this may sound rather trivial for most users, but I intend to install gromacs 3.3.1 on a dual core machine and I want to be sure what to do. Could anyone indicate me some online tutorial to do so (as well some simulation examples)? Is this considered parallelization (with

Re: [gmx-users] Gromacs setup on dual core machine

Kpiwara De X-nelo wrote: Hello You'll need FFTW (fftw.org ) LAM/MPI (lam-mpi.org ) and gromacs sources Download the 3 packages start with the Lam/MPI (configure , make , make install) Then fftw (the 2.1.5 version is needed, the 3.2 supports it but is still

[gmx-users] Install on a 64 bit dual core machine - Debian linux

ights? Thanx in advance. -- ___ Ricardo Soares Post-graduation Student in Biological Physics University of Sao Paulo - USP Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP Phone: 55 (16) 3602-4840 Curriculum Lattes - http://lattes.cn

[gmx-users] Co2.pdb

Hello, Your atoms coordinates are too far away from each other. Try to paste the text below into a new text file. Make sure to rename it to a .pdb extension. Voila! Cheers. Ps. This is a Methan molecule. HEADER METHANE HETATM1 C 1 0.257 -0.

[gmx-users] Concatenate TPR files after restart

Hello everyone, I've extended one previously finished simulation from 5 ns to 10 ns. Now I have two tpr files. How can I merge both of them in only one file? I'm asking this because I need to use g_hbond and I wanna analyze the whole trajectory. Best regardings. -- __

Re: [gmx-users] Concatenate TPR files after restart

There is no need to concatenate .tpr files; they contain structure and parameter information, and thus is does not make sense to add them together. To analyze the whole trajectory, supply g_hbond the starting .tpr file along with your trajectory file. -Justin -- Ok Jus

[gmx-users] How to build a custom protein (PDB file)

Hello everyone! I have a particular amino acid sequence and I wanna build a custom-shaped protein and make it a pdb file (I'm talking about non-realistic forms, like squares or a full extended chain). Can anyone indicate me some software for this task? Thanx! --

Re: [gmx-users] How to build a custom protein (PDB file)

Ok! I will give them a shot! Thanks! -- ___ Ricardo O. S. Soares Post-graduation Student in Biological Physics University of Sao Paulo - USP Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP Phone: 55 (16) 3602-4840 Curriculum Lat

[gmx-users] G_RMS for different simulations

Ok, solved it simply by using the confout.gro for another simulation instead of its tpr file. Thanks anyway! -- ___ Ricardo Oliveira dos Santos Soares Post-graduation Student in Biological Physics University of Sao Paulo - USP Faculty of F

[gmx-users] G_RMS for different simulations

Hi everyone, I need to compare a traj.xtc file from a simulation (say, A), with a starting structure from *another* simulation (say, B). The protein is the same, but the temperatures aren't. I tried the fallowing, with no success: g_rms -s simulation*A*.tpr -f simulation*B*.xtc Any ideas?

[gmx-users] G_RMS after Replica exchange

Hello everyone, I perform a simulation at 300K, then after 50 ns, I took the final structure and performed another one, but now at 274K. How can I compare this second trajectory's RMSD with the initial structure from the first simulation (300K)? If I compare with the first tpr file or the init