Re: [gmx-users] how to make h-bond existence map?

Hi, On Wednesday, 3. September 2008, minnale wrote: > Thanks Justin for your valuable suggestions > I have done the way you suggested. I gave command like this > g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) -num > .xvg -hbm .xpm it showed > Select a group: 15 > Selected 1

Re: Re: [gmx-users] how to make h-bond existence map?

Thanks Justin for your valuable suggestions I have done the way you suggested. I gave command like this g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) -num .xvg -hbm .xpm it showed Select a group: 15 Selected 15: 'MainChain+H_&_r_22_50_56_121_22' Select a group: 15 Sel

[gmx-users] Problems with molecular dynamic investigation of an cyclic peptide nanotube

Hi, Gromacs users, I was caught by a big problem with molecular dynamic investigation of an cyclic peptide nanotube. When i do energy minimization with em.mdp parameter file as follows, it gave out a warning: Warning: 1-4 interaction between 135 and 144 at distance larger than 1 nm. I ignored it a

Re: [gmx-users] Visualizing g_sdf on a Mac

Hello, somebode told me, that VMD is also able to render the SDF plot. However I have not tested it so far. Good Luck, Flo On 03.09.2008, at 01:28, Matt Wyczalkowski wrote: I'm looking into using g_sdf for analysis. The instructions suggest using gOpenMol: "The output will be a binary 3

Re: [gmx-users] Parameters for DNA bases

Jeff Woodford wrote: Hi all, Forgive me if this is a stupid question, but: I am attempting to simulate the interaction between a peptide and a DNA strand using the OPLS/AA force field. However the parameters for the DNA bases don’t appear to be included. Where might I find these paramete

[gmx-users] g_rotacf

Dear users, I have given a command like the following to calculate the rotational auto correlation function: g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b -e 1 -n .ndx -d I want to use the second order Legendre polynomial to fit. I integrated the resulting .xvg file, to obtain the cor

[gmx-users] Visualizing g_sdf on a Mac

I'm looking into using g_sdf for analysis. The instructions suggest using gOpenMol: "The output will be a binary 3D-grid file (gom_plt.dat) in the .plt format that can be be read directly by gOpenMol." However, the gOpenMol web site does not distribute Mac binaries (nor source). I am using Mac O

[gmx-users] g_rotacf

Dear users, To calculate the rotational auto correlation functions, the command mentioned in the maual is: g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa -beginfit -endfit what are the -nparm and -fa options are meant for ? Also do we need to use -fitfn option to obtain the rotational auto c

[gmx-users] Parameters for DNA bases

Hi all, Forgive me if this is a stupid question, but: I am attempting to simulate the interaction between a peptide and a DNA strand using the OPLS/AA force field. However the parameters for the DNA bases don't appear to be included. Where might I find these parameters suitable for adapting to

[gmx-users] Re: charge atoms

gurgo> Hi All gurgo> I am trying to analyze the dynamics of polymer of GlcN residues using gurgo> ffG53a6 force field. gurgo> I made a new building block in .rtp file, but I havenґt the charge of some gurgo> atoms. gurgo> Which is the best procedure to obtein new charges? gurgo> Someone has experi

Re: [gmx-users] charge atoms

Hi, When the question is "what's the dynamics of a GlcN chain?", it is quite important to have a proper set of parameters. If the question is "what would a protein do when something resembling a GlcN chain is inserted (e.g. Lysozyme)?" then you may get away using a set of parameters derived from a

Re: [gmx-users] G_RMS after Replica exchange

Hi Ricardo, Please give your exact command lines and the error you're refering to. The way it is now, you provide too little information for us to assess the origin of your problem. Cheers, Tsjerk On Tue, Sep 2, 2008 at 8:53 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote: > Hello everyone, > > I

Re: [gmx-users] how to make h-bond existence map?

minnale wrote: Hi all, I am confusing while calculating hydrogen bonds of my protein.I issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt mention .ndx because I wanted to know the H-bonds in whole protein system. I have selected mainchain+H two times, command went fine and it s

[gmx-users] Re[4]: Using Morse potentials with ENCAD force field

    1NIT     N1    1  -0.552   0.004  -0.026     1NIT     N2    2   0.552  -0.004   0.026   2.0  2.0  1.2 Andy, If I were your system, I would explode immediately and never let run myself again. b0 (N-N) = (0.552+0.552)=1.104 nm. How should the system behave with such unrealisti

[gmx-users] how to make h-bond existence map?

Hi all, I am confusing while calculating hydrogen bonds of my protein.I issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt mention .ndx because I wanted to know the H-bonds in whole protein system. I have selected mainchain+H two times, command went fine and it showed Select

[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

Re: [gmx-users] charge atoms

[EMAIL PROTECTED] wrote: Hi All I am trying to analyze the dynamics of polymer of GlcN residues using ffG53a6 force field. I made a new building block in .rtp file, but I haven´t the charge of some atoms. Which is the best procedure to obtein new charges? For some general information, refer h

[gmx-users] charge atoms

Hi All I am trying to analyze the dynamics of polymer of GlcN residues using ffG53a6 force field. I made a new building block in .rtp file, but I haven´t the charge of some atoms. Which is the best procedure to obtein new charges? Someone has experience about this? Any help would be appreciated Ca

[gmx-users] testing Tip5p water

Dear all, a similar problem was proposed in this list in 2002: http://www.gromacs.org/pipermail/gmx-users/2002-August/002339.html I cannot solve my problem, when testing tip5p in gromacs. T( c) density((g/cm^3) -E(kcal/mol) REF125.0 0.999

[gmx-users] Re: Re[2]: Using Morse potentials with ENCAD force field

You have problems with your force field. If you send me all the files describing your system I'll try to see what really happens when I have free time.. 2008/9/2 Andy Shelley <[EMAIL PROTECTED]>: > I have been able to get the molecules to become more homogenous. The problem > was I wasn't runnin

Re: [gmx-users] Bonds missing in VMD visualization

So I was testing on VMD the C-CL bond distance to draw a bond. Actually, the limit was a disturbing 1.80A ! So close to the 1.81A you need :( Solutions ! 1) Use "dynamic bonds representation" and set the cut-off to 1.81 or more 2) Find where VMD sets it's standard cutoff for bonds and set it to

[gmx-users] Re: Re[2]: Using Morse potentials with ENCAD force field

I have been able to get the molecules to become more homogenous. The problem was I wasn't running the system long enough. I looked at the energy of the system though and am getting very large fluctuations. The system was ran with the initial temperature set at 300K by setting inital velocities, bu

Re: [gmx-users] Strange behavior from steepest descents

I may have discovered the solution to my own problem, so I'll post it here just as a follow-up. It appears that inflation of a POPE bilayer causes extremely favorable interactions within the PE headgroup, causing the amine moiety to collapse into the phosphate. This generates the near infini

[gmx-users] RE: Potential energy of POPC (minnale )

-- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080902/72ce4b1d/attachment-0001.html -- -- Dr. Carsten Selle University of Leipzig Institute for Experimental Physics I PW

[gmx-users] problem with mpirun

Hi, Gromacs users, This command "grompp_ompi -np 6 -f pr_10_200.mdp -c after_em_newton_1000.gro -p all.top -o pr_10_100.tpr -po mdrun_pr_10_100.mdp" run normally. But when i run the next command "mpirun -np 6 mdrun_ompi -s pr_10_100.tpr -c after_pr_10_100.gro -o after_pr_10_100.trr -e after_pr

Re: [gmx-users] Fatal error: Atomtype 'OWT3' not found!

Manoj Kumar Singh wrote: I am getting following error while setting up a minimization. --- Program grompp, VERSION 3.3.3 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'OWT3' not found! --- I have no idea wh

Re: [gmx-users] G53a6 parameterization for DPPC

On Tue, Sep 02, 2008 at 09:48:58AM +0200, Ángel Piñeiro wrote: > > My conclusion is that this parametrization should not be used, at least for > DPPC bilayers… and I would question also the use of DMPC with G53a6... > although I am not sure with this lipid. I want to ask for advice from > experts

Re: [gmx-users] Potential energy of POPC

minnale wrote: Hi all, I have done popc simulation for 5ns and calculated potential energy of POPC. The values started from -269000 kj/mol reduced to -272000 kj/mol. Could you please tell me 1.is it require to extend my simulation from 5ns? What properties are you interested in? Potenti

Re: [gmx-users] Bonds missing in VMD visualization

Thank you for your reply. I tried the following: VMD computes distances between pairs of atoms to "draw" a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. In 1,1,1-trichloroethane

[gmx-users] G53a6 parameterization for DPPC

This is to report some results that I have been recently obtaining with the G53a6 parameterization of DPPC and also to ask for advice. I have read in the mailing list that perhaps this parameterization is worse than that of Tieleman/Berger to reproduce bilayer properties but I didn’t think that dif

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

Ran Friedman wrote: As far as I know most of this stuff is being worked on by Berk Hess. In standard GROMACS you can use tabulated potentials for everything bonded and non-bonded, if that helps overcome the harmonic-only problem. In which version are tabulated potentials available? non-bonded

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

> As far as I know most of this stuff is being worked on by Berk Hess. > In standard GROMACS you can use tabulated potentials for everything > bonded and non-bonded, if that helps overcome the harmonic-only problem. In which version are tabulated potentials available? Thanks, Ran ___

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

Suman Chakrabarty wrote: Dear Tsjerk, thanks for your response. It makes sense. Once I am through with my current project that I am busy with, I might take up this implementation more seriously and actively. By that time I need to be in a position to be able to look into the Gromacs source

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

Dear Tsjerk, thanks for your response. It makes sense. Once I am through with my current project that I am busy with, I might take up this implementation more seriously and actively. By that time I need to be in a position to be able to look into the Gromacs source code and understand how everyth

Re: [gmx-users] Fatal error: Atomtype 'OWT3' not found!

Manoj Kumar Singh wrote: I am getting following error while setting up a minimization. --- Program grompp, VERSION 3.3.3 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'OWT3' not found! --- I have no idea why

Re: [gmx-users] potential energy ACF

Vitaly Chaban wrote: Hello, Please give me a hint. Is it possible to calculate an autocorrelation function of interaction energy between some groups in a system using gromacs standard tools? For example, ACF of interaction energy between protein and water. Thanks. g_energy -- David van der

[gmx-users] potential energy ACF

Hello, Please give me a hint. Is it possible to calculate an autocorrelation function of interaction energy between some groups in a system using gromacs standard tools? For example, ACF of interaction energy between protein and water. Thanks. -- Vitaly

[gmx-users] Fatal error: Atomtype 'OWT3' not found!

I am getting following error while setting up a minimization. --- Program grompp, VERSION 3.3.3 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'OWT3' not found! --- I have no idea why this is happening and looki

Re: [gmx-users] How to calculate scaling factors in the LIE equation

Hi, There's no prescription. Check the papers by Åqvist. Ran. Raghunadha Reddy Burri wrote: > Dear all, > > I hope van der waals and electrostatic scaling factors in the LIE > equation (g_lie) are system dependent (Ref: DK Jones-hertzog et al. > 1996). Any one please give me a suggestion to calcul

Re: [gmx-users] COM monitoring

g_traj On Tue, Sep 2, 2008 at 5:52 AM, rams rams <[EMAIL PROTECTED]> wrote: > Dear users, > > Is it possible to monitor the center of mass motion of a protein using > gromacs tools since this is the one to monitor in most of the dynamical > studies of the protein. > > Thanks in advance. > > Ram. >

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

Hi Suman, I think this discussion would be better placed on the developers-list (but I'm not sure you're subscribed to that so I'll keep it here). First, I think it's not a good idea (and it's against Gromacs philosophy) to remove functionality, as this will disallow repeating earlier studies. Sec