Re: [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)

[EMAIL PROTECTED] wrote: Hi all, I'm having trouble with the compilation of GROMACS on a Mac Pro (OS X). It's a machine with two Quad-Core Intel Xeon, so 8 nodes in all. As compiler I used the programs delivered with the Xcode tools 3.0 and for parallelisation the LAM/MPI package delivered with

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 116

Dear Rebeca, I modestly build a program based on antechamber and inspired mostly by amb2gmx.pl: http://code.google.com/p/acpypi/ I hope it can be a bit easier to use. You should also take a look in the tutorials I put there, because the may give you an idea why you are facing problems (I

RE: [gmx-users] amb2gmx for big systems

Dear Rebeca, I modestly build a program based on antechamber and inspired mostly by amb2gmx.pl: http://code.google.com/p/acpypi/ I hope it can be a bit easier to use. You should also take a look in the tutorials I put there, because the may give you an idea why you are facing problems (I

Re: [gmx-users] analysizing the sam.edo script?

xi zhao wrote: Dear users: I want to analyze the EDS (essential dynamics sampling ) results (sam.edo file),though the website and manual both show that parse_edo can do it, I do not know how to get it,because I can not find it in the website. Please help me! I don't seem to have a

[gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue

sunita gupta wrote: Hello I have a query that how to do PCA which further includes *plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue*. I read in many articles that this can be done using gromacs. I did my MD simutaion using charmm forcefield and

Re: [gmx-users] dimerization problem

Hi Prasun, As a side-note to the replies of Justin and Florian, why not take the following approach?: 1. run pdb2gmx on the monomer, giving structure and topology for one unit (2. energy minimize in vacuum) 3. use editconf to make a transformed copy of the monomer -- now, you know for sure that

Re: [gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue

Hi, A displacement is not a fluctuation. Displacement is also relational, so you'll have to specify with respect to what. Likely you'd interpret displacement with respect to the mean structure, which by definition is at zero on a given principl axis. But in that case, the displacement is more

[gmx-users] Testing (was: Tyrosine problems again)

[EMAIL PROTECTED] wrote: Roll back to gcc 3.x. There is information available that says something like don't use gcc 4.x, it is broken, but I stand by my previous comments that it is unfortunate that it is up to the end user to search the gromacs archives to find this out, not withstanding

[gmx-users] Re: Putting more than one peptide

Hi I am doing 5 peptide simulation. 1. First i am defining a box using editconf editconf -f 1st.gro -o box1.gro -bt cubic -box 6 -d 1.1 then for inserting the next peptide i am using genbox genbox -cp box1.gro -ci 2nd.gro -nmol 1 -o box2.gro -seed 24 -try 100 and same for the subsequent 3

Re: [gmx-users] Re: Putting more than one peptide

[EMAIL PROTECTED] wrote: Hi I am doing 5 peptide simulation. 1. First i am defining a box using editconf editconf -f 1st.gro -o box1.gro -bt cubic -box 6 -d 1.1 then for inserting the next peptide i am using genbox genbox -cp box1.gro -ci 2nd.gro -nmol 1 -o box2.gro -seed 24 -try 100 and

Re: [gmx-users] Testing

David van der Spoel wrote: [EMAIL PROTECTED] wrote: Roll back to gcc 3.x. There is information available that says something like don't use gcc 4.x, it is broken, but I stand by my previous comments that it is unfortunate that it is up to the end user to search the gromacs archives to

Re: [gmx-users] Order parameters of lipid

minnale wrote: Thanks to Justin for his suggestion I tried the way mentioned in http://wiki.gromacs.org/index.php/make_ndx. I made index file with seperate groups and feed to g_order command g_order -f .xtc -s .tpr -od scd.xvg -o ord -n .ndx Group0 (C34) has 128 elements

[gmx-users] query about essential dynamics

Dear all,       I performed essential dynamics analysis on two proteins at different temperatures ranging from 300 K to 473 K; subsequently I tried to calculate RMSIP (root mean square inner product) to determine the subspace overlap between two different trajectories at different

Re: [gmx-users] Order parameters of lipid

Yes, I never managed to get a later version of g_order to function properly.  I only ever get the -Sg and -Sk outputs, no matter WHAT I put in the index files.  I've just kept an old version of gromacs on the machine I use for analysis.  A copy of 3.2.1 should be quite easy to download, and

Re: [gmx-users] Order parameters of lipid

Alan Dodd wrote: Yes, I never managed to get a later version of g_order to function properly. I only ever get the -Sg and -Sk outputs, no matter WHAT I put in the index files. I've just kept an old version of gromacs on the machine I use for analysis. A copy of 3.2.1 should be quite easy

[gmx-users] Re: Putting more than one peptide

1. First i am defining a box using editconf editconf -f 1st.gro -o box1.gro -bt cubic -box 6 -d 1.1 then for inserting the next peptide i am using genbox genbox -cp box1.gro -ci 2nd.gro -nmol 1 -o box2.gro -seed 24 -try 100 and same for the subsequent 3 peptides. So in this way when i am

[gmx-users] Testing

This type of notification is a good idea, although I would suggest a few things. - Find a way to make this message visible to people who script their installation and redirect their output to log files. For example, if I get executable binaries and I can't find the word error or warning in

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 5

Thanks Justin for your promt reply, whatever you told is correct, with same .xtc , .tpr , .ndx files I have used in gromacs version 3.3 It is working. Thanks alot once again. minnale wrote: Thanks to Justin for his suggestion I tried the way mentioned in

[gmx-users] Testing

I did actually run the test set on an earlier installation of gromacs on this computer and I just ran it again to see what the output would be. The only error I receive is in the dec+water files, which is described in the wiki as 'unimportant' (I did check the #s and they are similar to what

Re: [gmx-users] Testing

David Chan wrote: I did actually run the test set on an earlier installation of gromacs on this computer and I just ran it again to see what the output would be. The only error I receive is in the dec+water files, which is described in the wiki as 'unimportant' (I did check the #s and they are

[gmx-users] Testing

I am reinstalling now - hopefully everything will work after that! Please do let this list know how it works out, either way, and even if you do submit a bugzilla (which would also be great). I am quite interested to know what you find. Chris.

[gmx-users] Fwd: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue

-- Forwarded message -- From: sunita gupta [EMAIL PROTECTED] Date: Fri, Aug 1, 2008 at 1:12 PM Subject: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue To: [EMAIL PROTECTED] Hello I have done 15 ns MD to study the effect of point

Re: [gmx-users] Testing (was: Tyrosine problems again)

On Fri, Aug 1, 2008 at 4:47 AM, David van der Spoel [EMAIL PROTECTED]wrote: [EMAIL PROTECTED] wrote: Roll back to gcc 3.x. There is information available that says something like don't use gcc 4.x, it is broken, but I stand by my previous comments that it is unfortunate that it is up to

Re: [gmx-users] Testing

Roland Schulz wrote: On Fri, Aug 1, 2008 at 4:47 AM, David van der Spoel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Roll back to gcc 3.x. There is information available that says something like don't use

Re: [gmx-users] Testing

On Fri, Aug 1, 2008 at 3:48 PM, David van der Spoel [EMAIL PROTECTED]wrote: Roland Schulz wrote: On Fri, Aug 1, 2008 at 4:47 AM, David van der Spoel [EMAIL PROTECTED]mailto: [EMAIL PROTECTED] wrote: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Roll back to gcc 3.x.

[gmx-users] Testing (was: Tyrosine problems again)

Hello once again As per the suggestions, I went ahead and installed an older version of the gcc compiler: version 3.4. I then re-installed fftw and gromacs3.3.3 using the following commands: ./configure --enable-float --enable-threads --enable-sse --prefix=/home/david/fftw-gcc3

[gmx-users] dihedral potential OPLSAA force field

Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) (which are identical to those

[gmx-users] dihedral potential OPLSAA force field (correction)

in my previous post, for the values of the Ryckaert-Bellemans parameters (in kJ/mol) that i calculated dihedral C0 C1 C2 C3 C-C-C-C3.56686 -1.889076 1.313776 -2.33467 should be: dihedral C0 C1 C2

Re: [gmx-users] Testing (was: Tyrosine problems again)

[EMAIL PROTECTED] wrote: Hello once again As per the suggestions, I went ahead and installed an older version of the gcc compiler: version 3.4. I then re-installed fftw and gromacs3.3.3 using the following commands: ./configure --enable-float --enable-threads --enable-sse