Re: [gmx-users] ascii Covariance matrix

search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arneh Babakhani McCammon Lab De

Re: [gmx-users] Average Structure outputted from g_rmsf

/Erik > > 20 sep 2007 kl. 17.18 skrev Arneh Babakhani: > >> Great, got it, thanks for the suggestion, appreciate the input, >> >> Arneh >> >>> Arneh Babakhani wrote: >>>> Hi, >>>> >>>> When outputting the average structure fro

Re: [gmx-users] Average Structure outputted from g_rmsf

Great, got it, thanks for the suggestion, appreciate the input, Arneh > Arneh Babakhani wrote: >> Hi, >> >> When outputting the average structure from g_rmsf using the -ox option, >> some of my residues in that average structure pdb have awkward >> coordinates

Re: [gmx-users] Average Structure outputted from g_rmsf

Ok, thanks, I figured as much, was wondering if there was an option perhaps in g_rmsf that would produce a "minimized" average structure . . . I guess not, Arneh > Hi, > > On Thursday, 20. September 2007 16:15, Arneh Babakhani wrote: >> Hi, >> >> When

[gmx-users] Average Structure outputted from g_rmsf

Hi, When outputting the average structure from g_rmsf using the -ox option, some of my residues in that average structure pdb have awkward coordinates (when you visualize it in VMD, it looks very strange). Sometimes atoms are placed very close to each other, with really bad bond angles. I suppos

[gmx-users] g_rmsf and the -fit option , calculating average structures

I see to calculate the average structure of a protein in a trajectory minus any rotational + translational effects, using g_rmsf. Does the -fit option (default yes) eliminate rot + trans contributions? Or must one use trjconv first, to convert the trajectory to some reference frame eliminati

[gmx-users] output of g_covar with -ascii option , and the format of covar.dat

A = [ x1 0 0 x2 0 0 x3 0 0 y1 0 0 y2 0 0 y3 0 0 z1 0 0 z2 0 0 z3 0 0 0 x1 0 0 x2 0 0 x3 0 0 y1 0 0 y2 0 0 y3 0 0 z1 0 0 z2 0 0 z3 0 0 0 x1 0 0 x2 0 0 x3 0 0 y1 0 0 y2 0 0 y3 0 0 z1 0 0 z2 0 0 z3 ]; and B = [ x1 y1 z1 x2 y2 z2 x3 y3 z3 ] Arneh

Re: [gmx-users] Correlation Matrix Calculation

100 > atoms. > > Hope it helps, > > Tsjerk > > On 9/5/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: >> Thanks Tsjerk, >> >> One other question, regarding the covar.dat file (the covariance matrix >> that's outputted when using the -ascii f

Re: [gmx-users] Problems using mdrun_d

nd paste the output here for us to continue our help? On 9/6/2007 5:43 AM, Arneh Babakhani wrote: Hi, I've compiled a mpi double-precision version of mdrun_d. I'm trying to use it, but I get the following error. Any ideas what the 'symbol lookup error' is? -

[gmx-users] Problems using mdrun_d

Hi, I've compiled a mpi double-precision version of mdrun_d. I'm trying to use it, but I get the following error. Any ideas what the 'symbol lookup error' is? -- [EMAIL PROTECTED] Window-1]$ mpirun -np 4 mdrun_d -np 4 -s UmbrellaMD.tpr -o UmbrellaMD -c AfterUmbrellaMD

Re: [gmx-users] Correlation Matrix Calculation

h, Yes. As you should be able to recall, the (linear, not "generalized") correlation is formally given as: cor(x,y) = cov(x,y) / ( sqrt(var(x))*sqrt(var(y)) ) The diagonal elements of the covariance matrix give the variances... Cheers, Tsjerk On 8/31/07, Arneh Babakhani <[EMAIL P

Re: [gmx-users] Correlation Matrix Calculation

m_ij > by sqrt(m_ii)*sqrt(m_jj). > > Cheers, > > Tsjerk > > On 8/31/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: >> Can anyone briefly recommend a procedure for calculating the correlation >> matrix (not the diagonalized covariance matrix, as done by g_co

Re: [gmx-users] Correlation Matrix Calculation

Yes, I have seen this, had trouble compiling it. Does it matter what version of gromacs you're trying to compile it with? > Hi, > > > On Friday, 31. August 2007 05:14, Arneh Babakhani wrote: >> Can anyone briefly recommend a procedure for calculating the correla

[gmx-users] Correlation Matrix Calculation

Can anyone briefly recommend a procedure for calculating the correlation matrix (not the diagonalized covariance matrix, as done by g_covar) of a specified group? In particular, I'm looking to calculate the covariance matrix, as specifed in the Karplus paper (Proteins: Vol 11:205-217, 1991), where

[gmx-users] Using g_covar to calculate an average structure from a trajectory

Hi , I'd like to use g_covar to calculate the average structure of a trajectory. But at the moment, I'm not interested in any of the eig. value/vector data (which takes a considerable amount of time to calculate). Was wondering: Is there a way to suppress the eig. value/vector/covar matrix

Re: [gmx-users] Re: question about free energy. Gromacs user

> > Maybe it should be obvious, but (a) why are you constraining two > distances, and (b) are you sure your constraints aren't going to muck > with the internal degrees of freedom for the ligand? I would think one > would like to pull the ligand out of the receptor along some > particular directio

Re: [gmx-users] Using editconf to center on 0 0 0 , then using genbox

ensions of the box? (which are 6 6 6). The dimensions are irrespective of the centering of the box, right? [I know this seems a little trivial. I'd like to have my molecule centered at 0 0 0, b/c I'll be collecting coordinates later and it'll just make my math easier.] >

Re: [gmx-users] Using editconf to center on 0 0 0 , then using genbox

using editconf. > Arneh Babakhani wrote: >> Hi, >> >> I'm using editconf to center my sytem about the origin (0 0 0). No >> problem there. >> >> But then when I use genbox to solvate the resulting structure, the >> solvent >> is offset (no

[gmx-users] Using editconf to center on 0 0 0 , then using genbox

Hi, I'm using editconf to center my sytem about the origin (0 0 0). No problem there. But then when I use genbox to solvate the resulting structure, the solvent is offset (not centered about 0 0 0). Is there a way to correct this? Arneh ___ gmx-us

[gmx-users] editconf and the placement of the center of mass

Hi, In editconf, there's an option -center which allows you to place the geometrical center of your molecular at a desired location. I was wondering, is there an analogous option for the placement of the center of mass of a molecule? Thanks, Arneh __

Re: [gmx-users] Free energy calculation

Why not do a steered MD or umbrella sampling, where you start with the ligand in the binding pocket (in its correct conformation) and gradually pull it out. If done correctly, you should get a nice PMF. > Hello! > I need to calculate the free energy of complex formation between protein A > and li

Re: [gmx-users] which tool to use a measure a user-defined angle in a traj

g the ends of the axes (in your case, one C in one group and one O in the other) and the option -z, and it'll dump out a file of the angle those axes make with the z-axis. Don't be put off by the way it appears to be designed for helices. - Original Message From: Arneh Babakha

Re: [gmx-users] which tool to use a measure a user-defined angle in a traj

ing custom made analysis tools :) Alternatively, you could output the coordinates for the C and O using g_traj and use a script to calculate the angles with the z-axis, in case it's a single bond you're interested in. Cheers, Tsjerk On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote

[gmx-users] which tool to use a measure a user-defined angle in a traj

Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecul

Re: [gmx-users] Xenon non-bonded parameterization

Ok, So since there are no LJ on H in SPC/E, should we eliminate the line the line: XeH 1 1.992e-03 2.775e-06 to be more consistent??? David van der Spoel wrote: Morgan Lawrenz wrote: Hi all, I am doing umbrella sampling on 2 Xenon atoms in a solvated 3 nm box, with the at

Re: [gmx-users] g_wham and PMF problem

You have to collect all of the pdo files into one directory (and so you'll have to rename them if they all have identical names). Then zip them using gzip: gzip *.pdo Then you can use the g_wham code, something like: g_wham *.gz -bins 1000 -temp 300 -auto >> Hey Mark, >> Appreciate y

Re: [gmx-users] Non bonded parameters for Xe Xe Interactions

Great thanks, I had no idea such a tool existed. Also, if we're doing Xenon in water (spc) simulations, we have to parameterize the nonbonded interactions between OW and Xe, and H and Xe, right? That parameterization doesn't already exist, or does it? David van der Spoel wro

[gmx-users] Non bonded parameters for Xe Xe Interactions

Hi GMX community, We're doing some MD involving Xenon atoms. For our parameterization, we obtained sigma and epsilon (over kB) values of 3.975 Ang. and 214.7 K, from the following JCP reference: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA600012014006674

Re: [gmx-users] Error in Analysis Script RMSD

Ahh yes, you're right. The script is in the right directory, but for some reason it keeps reverting back to my home directory. I threw in a cd line to fix it. Thanks for the help! Arneh Mark Abraham wrote: Arneh Babakhani wrote: Hi, I'm experiencing an awkward error. I

[gmx-users] Error in Analysis Script RMSD

Hi, I'm experiencing an awkward error. I created an analysis script to calculate some RMSDs (I've pasted the script below). When I try to run the script, I get an error. The following is the output. Option Filename Type Description ---

[gmx-users] g_density : centering the density distribution plot

Hello, I'd like to use g_density to obtain a density distribution plot. Now, I'd like to place the center of that distribution on the zero of the horizontal axis. How do I so using g_density? From reading the manual, I see there's an option, "-center", which should do the trick. But I've

Re: [gmx-users] Building Topology of a Drug (using the ff of your choice)

o a beta server that will generate topology files consistent with the 43a1 FF. Cheers Mitch On Thu, 2007-02-15 at 17:48 -0800, Arneh Babakhani wrote: Hi , I'd like to build a topology of a Drug. I'm aware of the PRODRG website. But if my understanding is correct, on this website,

[gmx-users] Building Topology of a Drug (using the ff of your choice)

Hi , I'd like to build a topology of a Drug. I'm aware of the PRODRG website. But if my understanding is correct, on this website, you can only build using one forcefield (GROMOS87). How does one build a topology using a different force field (say for instance, oplsaa)? Is there a simple w

[gmx-users] using g_wham to read in pdo files

Hi, I was wondering if there's a way to read in only part of a pdo file, when using g_wham? For instance, I only want the first half of my pdo file. Does g_wham have any options that allow you to read in only the first half, or do I have to go in and delete the second half in the pdo file?

[gmx-users] g_wham and tol (tolerance) option

Hello, I was wondering if someone could provide a brief explanation of the -tol option (for setting the tolerance) in the g_wham tool. What exactly is this "tolerance", of what? (I couldn't find anything in the manual, nor the mailing list. If someone could point me in the right direction, I

Re: [gmx-users] membrane protein simulation

Diane, how big is the transmembrane part of your protein? Diane Fournier wrote: Hi gmx-users I am trying to set up an ED experiment with the low resolution structure of a membrane protein in the hope of generating NMR-like structures. >From what I have read until now, I know that I should

Re: [gmx-users] Minimization Issue - membrane inverted and system copied

C. Next time it may be better to center your system at the box center. Best, Tsjerk On 9/21/06, Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hi, I'm getting a quirky result from my minimization of my system (which consists of a small peptide in a membrane, solvated). Whe

[gmx-users] Minimization Issue - membrane inverted and system copied

Hi, I'm getting a quirky result from my minimization of my system (which consists of a small peptide in a membrane, solvated). When I look at the trr of the minimization (or the outputted structure after minization), I notice that my membrane has been inverted, and there are 4 copies of

Re: [gmx-users] make_hole vs. genconf

Great, thanks Chris! [EMAIL PROTECTED] wrote: I'd like to build some lipids around a peptide. Can I do so using genconf? (I know genconf can be used to build a membrane. I'm asking if genconf can be used to build a membrane around a solute, like a transmembrane protein?) "around"? No. I'

[gmx-users] make_hole vs. genconf

Dear GMX Users, I'd like to build some lipids around a peptide. Can I do so using genconf? (I know genconf can be used to build a membrane. I'm asking if genconf can be used to build a membrane around a solute, like a transmembrane protein?) I'm also aware of the make_hole tool. My que

[gmx-users] g_msd

Hi everyone, quick question about g_msd, When I execute:   g_msd -f FullMD1.trr -s FullMD1.tpr -n ForDiffusion.ndx -o test -lateral z At the end, the following is outputted in my terminal: D[   Protein] 0.1207 (+/- 0.0847) 1e-5 cm^2/s My index file only contains one group, labeled Protein

Re: [gmx-users] AFM Pulling

another node, the wrong ppa file was read. So the moral of the story is: When running AFM pulling in parallel, make sure that the names following "-pi" and "-po" differ! (something like, "-pi PeptidePull -po ExtraPeptidePull). Thanks! Arneh Arneh Babakhani wrote:

[gmx-users] AFM Pulling

Hi GXM Users, I'm trying to execute some AFM pulling.  My index file contains two groups, [TopPeptide]  and [DMPC].   I execute grompp, then when I try to execute mdrun: [EMAIL PROTECTED] SteeredMD]$ mdrun -s SMD-01.tpr -o SMD-01 -c AfterSMD-01 -e SMD-01 -g SMD-01 -pi PeptidePull.

[gmx-users] Constrained MD questions

Hello GMX Users, I have some specific questions about the constrained MD run options, as explained on page 116 (in the Special Topics section) of the GMX manual. 1. Regarding "constraint_direction = "What exactly is the meaning of the 3 values inputted here? Does 1.0 0.0 0.0 mean

[gmx-users] Solvating with glycerol

Hello, I have a small peptide that I'd like to solvate with glycerol (instead of water). I couldn't find a .gro and .itp file for glycerol in the top directory. I was wondering if anyone has such files and would be willing to share them? In looking at the other solvent .gro files (i.e. spc

Re: [gmx-users] PMF Calculations

Thanks. In GMX, is there a tool for integrating the mean force from an ensemble of configurations (in order to obtain the pmf)? Or does one have to do that by other means? Thanks, Arneh David van der Spoel wrote: Arneh Babakhani wrote: Hello, Can someone please describe the general

[gmx-users] PMF Calculations

Hello, Can someone please describe the general procedure for PMF (potential of mean force) calculations using GROMACS? Is there an analysis tool for this (I didn't see one), or a combination of tools? (Please note: I'm not asking for details. I'm just seeking a general method for calculatin

[gmx-users] Scripting Analysis tools in tcsh

Hello GMX users, (this may be more of a tcsh question, but here goes anyway). I'm trying to write a script to go through some trajectories and calculate hbonding. It looks like this: #!/bin/tcsh foreach number (1 2 3 4 5 6 7 8 9 10 11) g_hbond -f ../../FullMD/FullMD$number.trr -s ..

Re: [gmx-users] header of xvg file from GMX Analysis Tools

Thanks, I'll give it a shot . . . Arneh Mark Abraham wrote: Arneh Babakhani wrote: Sure . . . was just wondering if I could do it with an option in GMX . . . would be a lot easier to implement in the analysis scripts that I already have. Well I've never used Matlab, but I Googl

Re: [gmx-users] header of xvg file from GMX Analysis Tools

Sure . . . was just wondering if I could do it with an option in GMX . . . would be a lot easier to implement in the analysis scripts that I already have. Thanks, Arneh David Mobley wrote: You could write a little MATLAB function to strip the headers... On 6/27/06, Arneh Babakhani <[EM

[gmx-users] header of xvg file from GMX Analysis Tools

Hello, Is there an option I can use (with the various analysis tools) to prevent the output of the header information, when producing an xvg file? (In other words, to produce a data file, containing strictly the data). This is for plotting purposes in MATLAB. Thanks, Arneh

Re: [gmx-users] MPICH or LAM/MPI

Hi Carsten, thanks for the reply, good question. I can run it fine on as much as 4 processors, but nothing beyond that. Any idea why? Arneh Carsten Kutzner wrote: Hi Arneh, do you have the same problem on less processors? Can you run on 1, 2 and 4 procs? Carsten Arneh Babakhani wrote

Re: [gmx-users] MPICH or LAM/MPI

Hi All, Ok, I've successfully created the mpi version of mdrun. Am now trying to run my simulation on 32 processors. After processing with grompp and the option -np 32, I use mdrun with the following script (where CONF is the input file, NPROC is the number of processors): /opt/mpich/intel/bin/

Re: [gmx-users] problem with LAM

Hi, I was having this same problem.  I tried running like this: /opt/mpich/intel/bin/mpirun -v -np $NPROC -machinefile \$TMPDIR/machines ~/gromacs-mpi/bin/mdrun -np $NPROC -s $CONF -o $CONF -c After$CONF -e $CONF -g $CONF >& $CONF.job mpirun with the -v option (I'm not exactly sure what that

Re: [gmx-users] MPICH or LAM/MPI

to a missing LAM library: --- error while loading shared libraries: liblamf77mpi.so.0: cannot open shared object file: No such file or directory --- So make shure that this library can be found, probably in /path-to-lam-installation/lib Hope that helps, Carsten Arneh Babakhani wrote: Hello

Re: [gmx-users] off-diagonal of the tensor for pressure coupling should be zero??

Sunjoo, is there a particular reason why you want to you anisotropic pressure coupling? (I recently tried this myself, on a DMPC bilayer). Some of the key membrane physical properties (like thickness, area per lipid, order parameters) were distorted and did not agree with experimental evidence.

[gmx-users] afm rate , quick question about units.

Hello, in the GMX manual, on page 117, it states: afm rate1 = afm rate2 = The rate at which the spring moves in *nm/ps* for each group. In my ppa file, I specify: * afm rate1 = 1* But in the log file of my mdrun, it states: Pull rate: 1.00e+00 *nm/ns*. Force constant: 1.00e+03 k

Re: [gmx-users] MPICH or LAM/MPI

Hello, on this note, I'm having issues configuring and installing the mpi enabled mdrun. (see below). I keep getting a strange error: checking size of int... configure: error: cannot compute sizeof (int), 77 I've pasted the output below, and I've attached the config.log for reference.  I'm rea

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

So what does config.log tell you? Which test program does not compile? To be honest, I can't tell what's going on in config.log (I've pasted it below). I see a 'failed program' message with respect to confdefs.h , but I saw this during the configuration without mpi enabled (and it worked f

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Hi Francisco, was wondering if you ever resolved this issue? I too am trying to install gromacs mpi on our cluster, but have had no luck. I get the following error in the configure step: [EMAIL PROTECTED] gromacs-3.3.1]$ ./configure --enable-mpi --prefix=/home/ababakha/gromacs-3.3.1 checkin

Re: [gmx-users] gromacs parallel doesn't work

-g ResMD1 > & ResMD1.job &" Beniamino Arneh Babakhani ha scritto: grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top -o ResMD1 ; mpirun -np 4 mdrun -s ResMD1.tpr -o ResMD1 -c AfterResMD1 -e ResMD1 -g ResMD1 > & ResMD1.job & Mark Abraham wrote: Arneh

Re: [gmx-users] gromacs parallel doesn't work

grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top -o ResMD1 ; mpirun -np 4 mdrun -s ResMD1.tpr -o ResMD1 -c AfterResMD1 -e ResMD1 -g ResMD1 > & ResMD1.job & Mark Abraham wrote: Arneh Babakhani wrote: Hello, I'm having a similar problem, although my OS

Re: [gmx-users] gromacs parallel doesn't work

Hello, I'm having a similar problem, although my OS sees all 4 of my processors just fine. When I run mpirun -c 4 mdrun . . . all 4 of my processors are running, but only at 50% each. Furthermore, in present working directory, I see several backed up files: [EMAIL PROTECTED] TEMP]$ ls After

Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

parameters files an atom definition files (.rtp) Arneh Babakhani <[EMAIL PROTECTED]> wrote: *Hello, I'm getting the following warning when running grompp:* processing coordinates... Warning: atom names in ../BuildInitialStructure/NoBadWater.top and ../BuildInitialStructure/NoB

Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

x27;m more than willing to attach my gro and top file, so you can see them in their entirety. thanks, Arneh David van der Spoel wrote: Arneh Babakhani wrote: *Hello, I'm getting the following warning when running grompp:* processing coordinates... Warning: atom names in ../BuildI

[gmx-users] grompp warning: atom names don't match - with respect to solvent

Hello, I'm getting the following warning when running grompp: processing coordinates... Warning: atom names in ../BuildInitialStructure/NoBadWater.top and ../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW) Warning: atom names in ../BuildInitialStructure/NoBadWater.top and ../BuildI

Re: [gmx-users] Freezing part of the molecules!!!

Can you use this freezegroups function during a minimizaiton? (say if you wanted to minimize solvent around your protein, while keeping the protein fixed?) David van der Spoel wrote: Soren Enemark wrote: Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups t

Re: [gmx-users] index file for g_order

for the next carbon down. --- Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hi Alan, great, thanks, I suspected something like that. Then, is there a way to calculate the Scd order parameters for these carbons, given that there are no explicit hydrogens??? Arneh Alan Dodd wrote: The

Re: [gmx-users] index file for g_order

either side of each carbon to place the hydrogens, and hence calculate the order parameter. --- Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hello, Now with the g_order bug fixed (see bugzilla #84) , I'm trying to calculate the orderparameters for 13 carbon atoms of the the sn2 chain

[gmx-users] index file for g_order

Hello, Now with the g_order bug fixed (see bugzilla #84) , I'm trying to calculate the orderparameters for 13 carbon atoms of the the sn2 chain (carbons 2B thru 2N) of a DMPC membrane. So I create an index file, make a group for each type of carbon, then run g_order. The groups in the inde

Re: [gmx-users] g_order in Gromacs 3.3.1

FYI, the bug in g_order has been resolved, see: http://bugzilla.gromacs.org/show_bug.cgi?id=84 for details. Sukit Leekumjorn wrote: Dear GMX users, I have encounter some problem with g_order in Gromacs3.3.1. I noticed that tetrahedral order parameter has been added to the new version and for

Re: [gmx-users] Lipid Order Parameters - Calculating & Plotting

The bug in g_order has been resolved, see: http://bugzilla.gromacs.org/show_bug.cgi?id=84 Arneh Babakhani wrote: Hello GROMACS community, I was wondering if somebody could walk me through the process of calculating lipid order parameters (for a DMPC membrane), using the g_order analysis tool

[gmx-users] Steered Molecular Dynamics in GROMACS

Hello, Can anyone describe the general procedure for SMD in GROMACS? (i.e. how you designate which atoms are to be pulled, in what direction, and by what force). Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o

Re: [gmx-users] g_order in Gromacs 3.3.1

As have I. Very well, I have submitted a bugzilla (#84), Arneh Sukit Leekumjorn wrote: Concerning the problem with g_order in Gromacs 3.3.1. I did try fixing the problem as suggested, however, I could not get it to work. In the mean time, I just use g_order from 3.3 version. Sukit Arneh

Re: [gmx-users] Lipid Order Parameters - Calculating & Plotting

Hi Pedro, thank you for your prompt reply. I'm attempting to do what you suggested. 1). I create an index file, called sn2.ndx, which contains 14 groups, one group for each carbon type in the chain (labeled C2A, C2B, . . . C2N). 2) I then try to execute the following command: g_order -f Ful

Re: [gmx-users] g_order in Gromacs 3.3.1

Prof. Van Der Spoel, Regarding your suggestion here: Where exactly are lines 579 and 580 that one must modify? (I'm having this same error) Thanks, Arneh David van der Spoel wrote: Sukit Leekumjorn wrote: Dear GMX users, I have encounter some problem with g_order in Gromacs3.3.1. I no

[gmx-users] Lipid Order Parameters - Calculating & Plotting

Hello GROMACS community, I was wondering if somebody could walk me through the process of calculating lipid order parameters (for a DMPC membrane), using the g_order analysis tool? I've got a 5 ns trajectory and would like to make one of the classic order parameter plots: i.e. On the y-axis: the

[gmx-users] Lipid Order Parameters - Calculating & Plotting

Hello GROMACS community, I was wondering if somebody could walk me through the process of calculating lipid order parameters (for a DMPC membrane), using the g_order analysis tool? I've got a 5 ns trajectory and would like to make one of the classic order parameter plots: i.e. On the y-axis

[gmx-users] Pressure Coupling for Lipid Bilayers

Hello, Would the following be a reasonable way to implement semiisotropic pressure coupling, for a 128 DMPC membrane: ; Pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 1.0e-30 ref_p = 1.0 1.0 [I'm not asking whether this will prod

Re: [gmx-users] Genbox - Removal of Unwanted Waters

Great, thank you very much, will try it out, [EMAIL PROTECTED] wrote: If I have a solvated membrane and I want to extend the z dimension and add new waters there, this is what I do. The script could be modified to get rid of new waters in any x/y/z dimensions (around line 41 of the script). 1.

Re: [gmx-users] Genbox - Removal of Unwanted Waters

Thanks for the input. Is there a way to restrict the water from a certain space (in other words, to confine it a certain location)? Thanks, Arneh David van der Spoel wrote: Arneh Babakhani wrote: Hello all, How do you remove unwanted waters (or how do you prevent genbox from placing

[gmx-users] Genbox - Removal of Unwanted Waters

Hello all, How do you remove unwanted waters (or how do you prevent genbox from placing unwanted waters) after you solvate by genbox? This problem was posted once before, http://www.gromacs.org/pipermail/gmx-users/2005-December/018997.html but it doesn't seem like it was resolved. Is there an

Re: [gmx-users] Including and itp file, for a residue

this was the problem. I had the bloody inclusion files switched around! Thanks for your help! Arneh [EMAIL PROTECTED] wrote: appologies, CA is valid. Did you include lipid.itp before including dmpc.itp? I can't see what the problem is. Send your full commands and your top file. _

Re: [gmx-users] Including and itp file, for a residue

Hi, thank you for your input. I did that. Now I'm getting this error. --- Program grompp, VERSION 3.3.1 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'CA' not found! --- This d

[gmx-users] Including and itp file, for a residue

Hi, I'm trying to include the files dmpc.itp and lipid.itp , so that pdb2gmx will recognize it when building my membrane toplogy. Where exactly do I place the statement: #include "dmpc.itp" #include "lipid.itp" ??? I tried placing it in ffG43a2x.itp (that's the forcefield I'm using). But I

Re: RE : [gmx-users] segmentation fault in mdrun when using PME

Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you had any luck in trouble-shooting this? (I've pasted my mdp file below, for your reference).  Also running Gromacs 3.3.1 Arneh title = ResMD warnings

Re: [gmx-users] Error in Conjugate Gradient Minimization

Thank you for your input, I fixed it. You need to include: define = -DFLEXIBLE in the mdp file. Arneh Mark Abraham wrote: Arneh Babakhani wrote: Hello, *When trying to do CG minimization, I keep getting the following error:* Converted 0 out of 0 CUBICBONDS to morse bonds for

[gmx-users] Error in Conjugate Gradient Minimization

Hello, When trying to do CG minimization, I keep getting the following error: Converted 0 out of 0 CUBICBONDS to morse bonds for mol 8 processing coordinates... double-checking input for internal consistency... ERROR: can not do Conjugate Gradients with constraints (12309) There were 3 warni

[gmx-users] Fixed Atoms minimization and MD

Dear GROMACS users, Is it possible to run a minimization (or MD) with some atoms fixed, in GROMACS? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe r

[gmx-users] Building a peptide

Hello, I'm a new GROMACS user. Just a simple question: Can I use GROMACS to build a small peptide (6 residues), de novo? If so, how do I do this? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/li