[gmx-users] g_rms

Hi and thanks for answering to my previous question. Now I'm calculating the rmsd between two trajectories (-f2 option). One is made by 2200 frames and the other has 33 frames..Now I've some doubt about the output (rmsd.xvg), cause this file has only two columns with 2200 rows ...i was imaging

Re: [gmx-users] g_rms

andrea carotti wrote: Hi and thanks for answering to my previous question. Now I'm calculating the rmsd between two trajectories (-f2 option). One is made by 2200 frames and the other has 33 frames..Now I've some doubt about the output (rmsd.xvg), cause this file has only two columns with 2200

[gmx-users] g_order in GROMACS 3.3.2 and 3.3.1

Hello, gmx developer and users: After modifying the source code of g_order in GROMACS 3.3.1 with Bug #84 and compiling again, I got the error message when using g_order to calculate order parameteters of POPC bilayer. The error message is : grp 1 does not have same number of

[gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel)

Hi, I did the following, please let me know if more details are required regarding the architecture etc. - installed 3.3.1 as per instructions - downloaded the test set for 3.3.2 from the ftp site - source ~/gromacs-3.3.1/bin/GMXRC - cd gmxtest - ./gmxtest.pl simple The output for this is:

Re: [gmx-users] g_order in GROMACS 3.3.2 and 3.3.1

The g_order tool requires a unique sort of index group. There's lots of discussion about it documented in the list archives. In short, you need to use make_ndx to generate an index file that contains _only_ groups pertaining to the carbon atoms you want to analyze, separated by chain (i.e.,

Re: [gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel)

maria goranovic wrote: Hi, I did the following, please let me know if more details are required regarding the architecture etc. - installed 3.3.1 as per instructions - downloaded the test set for 3.3.2 from the ftp site - source ~/gromacs-3.3.1/bin/GMXRC - cd gmxtest - ./gmxtest.pl simple

Re: [gmx-users] g_rms

Hi, You should be getting such a 2200x33 matrix. My guess is that the command line or files that you're using are not what you think they are :-) my command line is g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin Note that the pdbs (traj and ref) have the same number of atoms (same

Re: [gmx-users] g_rms

andrea carotti wrote: Hi, You should be getting such a 2200x33 matrix. My guess is that the command line or files that you're using are not what you think they are :-) my command line is g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin If you read g_rms -h like I suggested last time,

Re: [gmx-users] g_rms

Hi again, If you read g_rms -h like I suggested last time, you'll see that -f2 and -s serve the same purpose with the former using a trajectory and the latter a single structure. That document doesn't say what happens when you use both... but the operation you're trying to do doesn't need

Re: [gmx-users] g_rms

andrea carotti wrote: Hi again, If you read g_rms -h like I suggested last time, you'll see that -f2 and -s serve the same purpose with the former using a trajectory and the latter a single structure. That document doesn't say what happens when you use both... but the operation you're trying

Re: [gmx-users] mdrun error after 2.6nS

Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS! I have searched in the archive,

Re: [gmx-users] mdrun error after 2.6nS

Hi Blaise, Check for the first occurrence of the error in the log file and match the atom numbers against your .gro file to see which residue is involved from the beginning. Also, do you have non-standard residues/metal ions? Tell more about the system and what you're trying to do. Best, Tsjerk

Re: [gmx-users] g_rms

So does the -Rmat option not produce a human-readable text file? Hi, unfortunately I can't see this option in g_rms. I'm using the v 3.3.1 and also on the reference page online there is not -Rmat. Am i missing something? Thanks Andrea ___ gmx-users

Re: [gmx-users] mdrun error after 2.6nS

Blaise Mathias-Costa wrote: Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS!

Re: [gmx-users] g_rms

andrea carotti wrote: So does the -Rmat option not produce a human-readable text file? Hi, unfortunately I can't see this option in g_rms. I'm using the v 3.3.1 and also on the reference page online there is not -Rmat. Am i missing something? Hmm, you're right. Installations that I know are

[gmx-users] Re: Is there a test set for GROMACS 3.3.1 ?

I could not see any obvious errors in either the log files or the out files in angles1 or angles125. grompp.out reports no warning or error either, do I did not change the maxwarn parameter anyway. Any other suggestions ? Or should I post the output or log files ? Then you have to do as it says

Re: [gmx-users] Re: Is there a test set for GROMACS 3.3.1 ?

maria goranovic wrote: I could not see any obvious errors in either the log files or the out files in angles1 or angles125. grompp.out reports no warning or error either, do I did not change the maxwarn parameter anyway. Any other suggestions ? Or should I post the output or log files ? Any

[gmx-users] getting a good .gro file from a pdb file while the topology is ready

Hi, I had a large bilayer in .gro and .top gromacs format files which I truncated to make a smaller bilayer, and added some more water molecules, using programs other than gromacs. The final output I have is a pdb file with complete solvation, and a topology file which I obtained from the

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

In message [EMAIL PROTECTED] (on 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic) wrote: Hi, I had a large bilayer in .gro and .top gromacs format files Bilayer? I believe there are some specific things for doing planar periodic boundary conditions (or planar infinite system

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

maria goranovic wrote: Hi, I had a large bilayer in .gro and .top gromacs format files which I truncated to make a smaller bilayer, and added some more water molecules, using programs other than gromacs. The final output I have is a pdb file with complete solvation, and a topology file which

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

Allen Smith wrote: In message [EMAIL PROTECTED] (on 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic) wrote: Hi, I had a large bilayer in .gro and .top gromacs format files Bilayer? I believe there are some specific things for doing planar periodic boundary conditions (or

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

On Wed, 3 Oct 2007 19:13:51 +0200 maria goranovic [EMAIL PROTECTED] wrote: Hi, I had a large bilayer in .gro and .top gromacs format files which I truncated to make a smaller bilayer, and added some more water molecules, using programs other than gromacs. The final output I have is a pdb file

[gmx-users] grompp not recognizing mdp file parameters

Hello, It seems that I am having a problem in that grompp is not recognizing the parameters that I enter into an mdp file, nor is it recognizing the text in the .top file. When I run a simulation, the output that I get is as follows: ERROR: invalid enum 'md' for variable integrator, using

RE: [gmx-users] protein in membrane

Shalom, The easy way is to remove lipids such that a hole in the membrane will form, put your protein in in run. Or you can try the protocol in Faraldo-Gomez, J. D., Smith, G. R., and Sansom, M. S. (2002) Setting up and optimization of membrane protein simulations. European Biophysics

[gmx-users] Re: getting a good .gro file from a pdb file while the topology is ready

Thank you all for the replies and help. The main reason I was messing with pdb2gmx, editconf and genbox was mainly to convert my pdb into a nice .gro format file, which I could input into grompp. I understand grompp can take a pdb file for input as well. Does it not need any box information, like

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

In message [EMAIL PROTECTED] (on 4 October 2007 04:04:05 +1000), [EMAIL PROTECTED] (Mark Abraham) wrote: Allen Smith wrote: In message [EMAIL PROTECTED] (on 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic) wrote: Hi, I had a large bilayer in .gro and .top gromacs format

Re: [gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready

In message [EMAIL PROTECTED] (on 3 October 2007 19:41:40 -0400), [EMAIL PROTECTED] (Justin A. Lemkul) wrote: You can use editconf to directly convert a .pdb file into .gro format. Good point. -Justin Quoting maria goranovic [EMAIL PROTECTED]: Thank you all for the replies and help. Quite

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

In message [EMAIL PROTECTED] (on 3 October 2007 19:09:54 -0400), [EMAIL PROTECTED] (Allen Smith) wrote: In message [EMAIL PROTECTED] (on 4 October 2007 04:04:05 +1000), [EMAIL PROTECTED] (Mark Abraham) wrote: Allen Smith wrote: Umm... the atom numbers (not just the numbers of residues) are going

[gmx-users] (no) superlinear Scaling on Opterons

Hello, there have been multiple reports on the list of superlinear scaling on AMD Opterons of the 200 series. We have recently purchased a small cluster with the following configuration for each compute node: - 2x Opteron 2218 (4 cores per node) - 2 GB RAM - Supermicro H8DM8 mainboard - Mellanox

[gmx-users] human readable input for g_covar

Hi: I am involving in a project to analyse the vibrational spectrum of a peptide. i am trying to do covariance analysis withnbsp; the velocity data in a .trr file using g_covar, since it doesn't take velocity by default, my plan is to output that in a human readable file and swat that with the