Re: [gmx-users] Correlation-Covariance

I'll submit it when the site is available. If anyone needs it urgently, send me a message off the list. Ran. Tsjerk Wassenaar wrote: > Hi, > > Otherwise, divide every element ij by sqrt(ii)*sqrt(jj). > > Cheers, > > Tsjerk > > On Wed, Jul 30, 2008 at 4:44 PM, Ran Friedman <[EMAIL PROTECTED]> wrot

Re: [gmx-users] g_sas, what's it all about?

On Wednesday 30 July 2008 12:58, David van der Spoel wrote: > Peyman Yamin wrote: > > Hello List! > > > > I use g_sas to calculate the solvent accessible surface area of some > > amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if > > the hydrophilic part is somehow not recogn

[gmx-users] Order parameters of lipid

I want to calculate order parameters of palmitoyl and oleyl chains of POPC which ran it for 5ns, so I have done below mentioned steps. 1. First I tried for Palmitoyl, so I made .ndx file by using make_ndx command and selected a C34|a 035|a C36.a C50. In index file the palmitoyl chain sele

Re: [gmx-users] Order parameters of lipid

minnale wrote: I want to calculate order parameters of palmitoyl and oleyl chains of POPC which ran it for 5ns, so I have done below mentioned steps. 1. First I tried for Palmitoyl, so I made .ndx file by using make_ndx command and selected a C34|a 035|a C36.a C50. In index file the pal

[gmx-users] Normal Mode Analysis in Double-Precision

Hi all! I'm trying to perform a normal mode (NM) analysis, but having trouble with the recommendation of first performing a double precision energy minimization before writing the Hessian. The calculation of the Hessian matrix is done using mdrun, and its diagonalization is done using g_nmeig

[gmx-users] amb2gmx for big systems

Hello, I am trying to convert a membrane-protein system from amber to gromacs using the script amb2gmx.pl (http://chemistry.csulb.edu/ffamber/tools.html). It is the dry system, only the protein and a membrane composed by DOPC, whose parameters I have got from Gaff. When I try: ./amb2gmx.pl -

[gmx-users] RE: value of d in editconf

Hi I am doing a 5 peptide(7 residue) simulation in a 5 nm cubic box. but during editconf i haven't given the option -d to specify the distance between the solute and the box. Now some of the atoms of my peptides are out of the box also is it normal? Does not applying -d is going to effect in any w

Re: [gmx-users] RE: value of d in editconf

[EMAIL PROTECTED] wrote: Hi I am doing a 5 peptide(7 residue) simulation in a 5 nm cubic box. but during editconf i haven't given the option -d to specify the distance between the solute and the box. Now some of the atoms of my peptides are out of the box also is it normal? Does not applying -

Re: [gmx-users] g_sas, what's it all about?

Peyman Yamin wrote: On Wednesday 30 July 2008 12:58, David van der Spoel wrote: Peyman Yamin wrote: > Hello List! > > I use g_sas to calculate the solvent accessible surface area of some > amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if > the hyd

[gmx-users] initial_configuration_sw_water

Hello everybody, I read somewhere that one can get the sw.gro file, by adding the shell and dummy particles (with the same coordinates as the oxygen) into the spc216.gro file. Is this right ? and when not how can I get the sw.gro file ? thank you for your time Sang Min _

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 75

Do the referenced functions (grads and inigms exist in your library? You might need to include the gmx.m Gerrit Hi Gerrit, I am having the same problem in 32-bit machine. The error message is : cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused - malign-double -funroll-al

Re: Re: [gmx-users] Order parameters of lipid

Thanks Justin for your prompt reply with better suggestion I have done like this 1.For index file Selected > a C34 3 34 :128 elements then > a C36 4 36 : 128 elements.. till C50( only C atoms) so index file contain [C34] atoms [36] atoms...[C50] 2. then I have typ

Re: [gmx-users] initial_configuration_sw_water

Sang-Min Park wrote: Hello everybody, I read somewhere that one can get the sw.gro file, by adding the shell and dummy particles (with the same coordinates as the oxygen) into the spc216.gro file. Is this right ? and when not how can I get the sw.gro file ? rename the tip5p.gro file.

Re: [gmx-users] Order parameters of lipid

Read about how to create the appropriate index file here: http://wiki.gromacs.org/index.php/make_ndx There are also several posts in the list archive on how to create the index file correctly. -Justin minnale wrote: Thanks Justin for your prompt reply with better suggestion I have done li

Re: [gmx-users] amb2gmx for big systems

Hi, On Thursday, 31. July 2008, Rebeca García Fandiño wrote: > Hello, > I am trying to convert a membrane-protein system from amber to gromacs > using the script amb2gmx.pl > (http://chemistry.csulb.edu/ffamber/tools.html). It is the dry system, only > the protein and a membrane composed by DOPC,

Re: [gmx-users] g_sas, what's it all about?

On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > On Wednesday 30 July 2008 12:58, David van der Spoel wrote: > >> Peyman Yamin wrote: > >> > Hello List! > >> > > >> > > >> > > >> > I use g_sas to calculate the solvent accessible surface area of some > >> > >

[gmx-users] dimerization problem

Dear user, I want to check the dimerization of a peptide chain having 227 residues.I am doing the following steps: 1. First i transformed the given peptide by 20 angstrom by modifying corresponding pdb file and save it as f1.pdb(say),original file given was 'f.pdb'(say) 2 .Now i run the pdb

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Hi, It's hard to know why you get a segmentation fault without further info. Did you ran the GMX tests after installation with double precision? Is everything all right there? Also, when exactly the system crashes? Is it straight when you start mdrun? Did you use both grompp and mdrun in double p

Re: [gmx-users] g_sas, what's it all about?

Peyman Yamin wrote: On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote: Peyman Yamin wrote: On Wednesday 30 July 2008 12:58, David van der Spoel wrote: Peyman Yamin wrote: > Hello List! > > > > I use g_sas to calculate the solvent accessible surface area of some > > amphiphiles.

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

hi, all 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 NAMD. I have converted my dcd

Re: [gmx-users] dimerization problem

prasun kumar wrote: Dear user, I want to check the dimerization of a peptide chain having 227 residues.I am doing the following steps: 1. First i transformed the given peptide by 20 angstrom by modifying corresponding pdb file and save it as f1.pdb(say),original file given was 'f

Re: [gmx-users] dimerization problem

Hi, On Thursday, 31. July 2008, prasun kumar wrote: > Dear user, > I want to check the dimerization of a peptide chain having 227 residues.I > am doing the following steps: > > 1. First i transformed the given peptide by 20 angstrom by >modifying corresponding pdb file and save it as >f1.p

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

Hi, On Thursday, 31. July 2008, sunita gupta wrote: > hi, all > > 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 si

Re: [gmx-users] g_sas, what's it all about?

Hi list, I wanted to post something about g_sas some time ago already, but didn't find time to. Here is the occasion. I believe g_sas does not actually compute the solvent accessible surface area (SASA, defined as the locus of the center of the probe sphere), but rather the molecular surfac

[gmx-users] Normal Mode Analysis in Double-Precision

Hi Ran, thanks for the reply I ran "make tests" after compiling with double precision, and it came out fine. Could it be that this, second, compilation might have caused some problems -- I had GROMACS compiled in single-precision, and it worked fine -- could compiling in double-precision a

[gmx-users] energy minimization

dear Ran I have checked it already can you please tell me the anoter way to do it. regards -- PRASUN (ASHOKA) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Inon Sharony wrote: > > Hi Ran, thanks for the reply > > I ran "make tests" after compiling with double precision, and it came > out fine. > > Could it be that this, second, compilation might have caused some > problems -- I had GROMACS compiled in single-precision, and it worked > fine -- could c

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Hi Ran. I looked up your suggestions, and got the following: 0. The parameters in the *.tpr file appear in " 0.e+00 " format. How can I tell if this is a float or double? Also, I could not see if the position coordinates of the molecule appear in the *.tpr file (and if so, if they a

Re: [gmx-users] g_sas, what's it all about?

Michel Cuendet wrote: Hi list, I wanted to post something about g_sas some time ago already, but didn't find time to. Here is the occasion. I believe g_sas does not actually compute the solvent accessible surface area (SASA, defined as the locus of the center of the probe sphere), but rath

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Inon Sharony wrote: > Hi Ran. > I looked up your suggestions, and got the following: > > 0. The parameters in the *.tpr file appear in " 0.e+00 " > format. How can I tell if this is a float or double? Also, I could not > see if the position coordinates of the molecule appear in the *.tpr >

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Ran Friedman wrote: > Inon Sharony wrote: > >> Hi Ran. >> I looked up your suggestions, and got the following: >> >> 0. The parameters in the *.tpr file appear in " 0.e+00 " >> format. How can I tell if this is a float or double? Also, I could not >> see if the position coordinates of th

Re: [gmx-users] Normal Mode Analysis in Double-Precision

I think we're getting somewhere... when I look at the *.tpr file, under the line nosehoover_xi: 0 I have the x[ 0] etc. lines, but they are as you described single precision should look like (the last two digits are all zeros). This is despite the fact that at the top it sa

RE: [gmx-users] definition of J-couplings in g_chi

Actually, both codes are fine. The problem turned out to be in the definition of the dihedral angles. Apologies for the false alarm, Abil > Date: Wed, 30 Jul 2008 09:36:38 +0200 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-u

RE: [gmx-users] amb2gmx for big systems

Hello, I am trying to translate the amber topology for a system membrane+protein (dry) to Gromacs. In view of the problems caused in amb2gmx.pl due to the size of the system (more than 600.000 atoms) I had tried another alternative: I created the amber topology for the protein and for a unique l

Re: [gmx-users] Normal Mode Analysis in Double-Precision

> >Could it be that this, second, compilation might have caused some >problems -- I had GROMACS compiled in single-precision, and it worked >fine -- could compiling in double-precision after the initial >single-precision overrun some files? I'm not sure anymore... > from experien

[gmx-users] Tyrosine problems again

Hi everyone I am having trouble (again) with my tyrosine residue. For some reason during early steps of my simulation, the ring of the tyrosine residue does not remain planar but rather is distorted - enough at times to look like a chair conformation. Earlier I thought this was a vsite=aromatics i

Re: [gmx-users] Tyrosine problems again

[EMAIL PROTECTED] wrote: Hi everyone I am having trouble (again) with my tyrosine residue. For some reason during early steps of my simulation, the ring of the tyrosine residue does not remain planar but rather is distorted - enough at times to look like a chair conformation. Earlier I thought t

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

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 the Xcode tools. The proble

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

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 the Xcode tools. The proble

[gmx-users] Tyrosine problems again

In the configuration log when I installed gromacs it indicates I'm using gcc version 4.3.0 20080428 (Red Hat 4.3.0-8). The log also shows lines of: checking dependency style of cc result: gcc3 Sorry, I don't know much about compilers etc; is this the answer you were looking for? David dicha

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

Hi, how did you compile Gromacs? You have to speficify --enable-mpi to configure. How did you run it? Give the exact command line. Roland On Thu, Jul 31, 2008 at 4:40 PM, <[EMAIL PROTECTED]> wrote: > Hi all, > I'm having trouble with the compilation of GROMACS on a Mac Pro (OS X). > It's a mac

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

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! -

[gmx-users] Tyrosine problems again

Is there really no way to ensure that the compilation was 'successful' during the configure/make/make install procedure? While a compiler problem is technically not a gromacs problem in that it is not an error of the gromacs developers, I think that this is still something that deserves to

[gmx-users] Tyrosine problems again

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 that it is a gcc-based

[gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?

Dear users: I want to know: in EDS (essential dynamics sampling), how to fix the eigenvector ,while the other degrees of freedom wiil be equilibrated. how to set up? using the :linfix" in make_edi ? Please help me! Thank you very much! - 雅虎邮箱，您的终

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] Problems with parallelisation of GROMACS on a Mac Pro (OS X)

Steffen, if don't intend to use GMX double precision, why not use Gromacs from FINK? It's all there. Use ommpi also, instead of lammpi (seems broken in Fink too). Then you can do something like: # with openmpi, for a dual core grompp -f em.mdp -c Complex_b4em.pdb -p Complex.top -o em.tpr -np 2 o