[gmx-users] position_restraints

Hi, Fatal error: [ file protein.itp, line 9 ]: Atom index (5) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints

[gmx-users] RE: Energy Minimization

Hi, I would allow flexible water by uncommenting the line define = -DFLEXIBLE and trying again; reducing the time step might also be required. Message: 4 Date: Mon, 18 Oct 2010 16:26:16 -0400 From: Sai Pooja

Re: [gmx-users] g_dipole ? => Calculate bond dipole moment for a molecule of multiple atoms by hand?

Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long a

Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

On 18/10/10 13:06, Mark Abraham wrote: On 18/10/2010 10:53 PM, ms wrote: On 18/10/10 03:30, Mark Abraham wrote: Mark, Thanks a lot for cc'ing me the bugzilla report. Do you think it is related to the problems I have? (well, for sure bugs can't help, but...) thank you! m. -- Massimo Sand

[gmx-users] Gibbs free energy of binding

Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

[gmx-users] Gromacs libraries: same for both single and double precision builds?

Hi, I'm installing GROMACS 4.5.1 on our Intel Nehalem/InfiniBand cluster and wish to install both single and double precision versions. Am I correct in thinking that the same libraries are built, both with or without "--enable-double", and it's just the binaries that are different (and there

Re: [gmx-users] position_restraints

#ZHAO LINA# wrote: Hi, Fatal error: [ file protein.itp, line 9 ]: Atom index (5) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move

Re: [gmx-users] Gibbs free energy of binding

shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTA

[gmx-users] Re: for gromacs

As I say continually, I am not a private tutor. Please keep all Gromacs-related correspondence on the gmx-users list. I am CC'ing this message there and would ask that any further discussion be held in this forum. Binding energy is not trivial to calculate, and will require some type of fre

[gmx-users] Gibbs free energy of binding

Shahab, Justin is entirely correct, you should read about potential of mean force calculations, the gromacs pull code, and the gromacs free energy code. However, an important question is if you can *converge* the free energy of macromolecular binding. If you don't know the bound state,

[gmx-users] amb2gmx.pl script ignores negative values of PK?

Hi all, There is a problem that I encountered when I was trying to manually verify the proper dihedral conversion from AMBER topology to GROMACS topology using amb2gmx perl script. Some of the dihedrals were set to zero by amb2gmx even if in the prmtop file they were not zero. This was happening f

[gmx-users] COM Pulling - Single Chain

Hi All, I was wondering if it is possible to pull on a single chain? I would like to anchor the C-terminus and pull the N-terminus and have a plot of pulling force vs displacement. I'm looking for more or less a yes or no answer, if you would like to elaborate then I won't complain :) Thank

[gmx-users] COM Pulling - Single Chain

re or less a yes or no answer, if you would like to elaborate then I won't complain :) Thanks, Joe -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/625c900f/attachment.html -- gmx-users ma

[gmx-users] Umbrella sampling with temperature and pressure coupling method problem

Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- gmx-users mailing

[gmx-users] Umbrella sampling with temperature and pressure coupling method problem

Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but probably you need to provide more

Re: [gmx-users] mdrun-gpu error

Hi Roland, I did as you suggested and it worked fine! Thanks, Renato 2010/10/15 Roland Schulz : > You should use the latest GROMACS version also for the GPU. Thus compile the > 4.5.1 for the GPU and run this. > > On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas wrote: >> >> Hi there, >> I have

Re: [gmx-users] Umbrella sampling with temperature and pressure coupling method problem

chris.ne...@utoronto.ca wrote: Use Langevin dynamics (the sd integrator) to control the temperature. You are sure to get the correct ensemble that way and if you are doing US then you can not extract dynamics anyway. Hopefully somebody else can address the pressure coupling for you, but pro

Re: [gmx-users] COM Pulling - Single Chain

a plot of pulling > force vs displacement. > > I'm looking for more or less a yes or no answer, if you would like to > elaborate then I won't complain :) > > Thanks, > Joe > > -- next part -- > An HTML attachment was scrubbed... > U

[gmx-users] COM Pulling - Single Chain

Warren, You're right that one can not use constraints if they are also using lincs on C-C bonds. However, constraining this bond is not necessary with a 1 fs timestep. Even while constraining C-C bond lengths, one can still use harmonic restraints instead (also from the pull code). Before get

[gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)

> Message: 6 > Date: Tue, 19 Oct 2010 09:30:47 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Umbrella sampling with temperature and >pressurecoupling method problem > To: Discussion list for GROMACS users > Message-ID: <4cbd9d87.6080...@vt.edu> > Content-Type: text/p

[gmx-users] Point Dipoles

Hi Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole to a molecule with an orientation? I've looked in the manual but find nothing or online. Also is there any provision for SSD [soft sticky dipole] water molecules? Thanks Brett-- gmx-users mailing listgmx-use

Re: [gmx-users] Point Dipoles

On 2010-10-19 18.40, Donovan B.T. wrote: Hi Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole to a molecule with an orientation? I've looked in the manual but find nothing or online. Also is there any provision for SSD [soft sticky dipole] water molecules? No an

Re: [gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)

DeChang Li wrote: Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] Umbrella sampling with temperature and pressurecoupling method problem To: Discussion list for GROMACS users ma

[gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf E

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd > Info) Using plugin psf for structure file /home/b

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect informatio

Re: [gmx-users] Tables with forcefield

On 27/09/10 21:18, Sai Pooja wrote: Thanks M! I am using the standard 6-12 tables available with the gromacs package. For -table and -tablep options to start with. I want to understand 1 thing. The forcefield files and the topology file specifies sigma and epsilon parameters. If I change the co

[gmx-users] Template file in gromacs4.5.1

Hi I had developed couple of post processing/analysis codes in earlier version of gromacs4.0.7. Now I have upgraded to gromacs4.5.1 and when I check its template file , its completely different that the earlier version. Does that mean old post-processing codes have to rewritten if I were to use n

[gmx-users] Re: Template file in gromacs4.5.1

Also, will there be any errors if I use trajectory computed by gromacs4.5.1 and use post processing code developed for gromacs4.0.7. I plan to keep both versions of gromacs installed on my system, until I get fully comfortable new version! On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak wrote:

[gmx-users] Amber-GS-S force field in Gromacs 4.5.1

Hello all, I noticed significant changes in my simulation results between running gromacs 4.5.1 with the included amber-gs-s force field and gromacs 4.0.7 with Eric Sorin's amber ports. I eventually figured out that the parameter files in the amberGS.ff directory are identical (up to whitespace

[gmx-users] Re: Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul) (Justin A. Lemkul)

> > > > Message: 5 > Date: Tue, 19 Oct 2010 13:06:42 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and >pressurecoupling method problem (Justin A. Lemkul) > To: Discussion list for GROMACS users > Message-ID: <4cbdd022.6020...@v

[gmx-users] Error on install Gromacs 4

Dear experts, I have just install gromacs 4.5.1 on my cluster (using CentOS that was install openmpi1.5, Platform MPI, fftw3, g77, gcc , g++) but I have problem with size of int : [r...@icstcluster gromacs-4.5.1]# ./configure --prefix=/shared/apps/gromacs --enable-mpi --enable-double checking bui

[gmx-users] g_dipole ? => ionic bond => how to determine the direction of ionic bond dipole moment ?

Hi molecule dipole is 48.0 sum of q_i x_i For a multiple-atoms molecule, the dipole moment of a covalent bond is a vector, parallel to the bond axis, For a multiple-atoms molecule, which includes a ionic bond, how to determine the direction of ionic bond dipole moment in theory ? How does Gromacs

[gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

united >> > atoms of most carbon groups, isn't the dipole moment too high? >> I think this is the average per molecule. You may need to run trjconv >> -pbc whole, because mdrun may break molecules in two parts, meaning that >> the molecule becomes as big as

Re: [gmx-users] Gibbs free energy of binding

Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a trajectory

Re: [gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

k molecules in two parts, meaning that > the molecule becomes as big as the box. > > > > > > > > > > > What does "will subtract their charge at their center of mass" this > mean? > > Why "will subtract their charge at their center of mass

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this