[gmx-users] how to identify the hydrophobic core residue to calcuate gyration

Hello guys, neone have idea how to mark which are the hydrophobic residue to supply with make index command and have to calculate the gyration curve. regards, Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/___

[gmx-users] polyalanine melt

Dear all,   I am running MD simulaiton using Gromacs for alpha-helilx polyalanine solution. The initial configuraiton of polyalanine peptide was generated using Discovery Studio. I follow the procedure below: 1: solvate the polyalanine in a water box 2: energy minimization (steep for 5000 steps a

[gmx-users] Abu added you as a friend on Reunion.com!

Hi, I looked for you on Reunion.com, but you weren't there. Please connect with me so we can keep in touch. -Abu Do You Know Abu? YES - Connect with Abu, and see who's searching for you http://smtp26.mail.reunion.co

[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder

Dear all, On transitioning from Gromacs version 3.3.3 to 4.0.3, I have encountered a segmentation fault (output below) preprocessing a constraint force calculation, while using the pull code with the "pull_geometry = cylinder" option in the mdp file. This problem appears is reproducible on

Re: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong wrote: Hi, I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command. --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 838 *Fatal e

[gmx-users] Invalid atom number 6415 in indexfile

Hi, I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command. *Here is the log from grompp:* Option Filename Type Description -f em.mdp Input, Opt! grompp input

Re: [gmx-users] pull code

avinash kumar wrote: Hello all, does anybody possess a sample of "pull.pdo" data file for pull codes. The pull.pdo file is output, are you sure that's what you want, or do you want a pull.ppa input file? Either way, enter "pull.pdo" or "pull.ppa" into the Search page for the archive and

[gmx-users] pull code

Hello all, does anybody possess a sample of "pull.pdo" data file for pull codes. -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] xtc groups. order of atoms

Please anybody soothe me. If one uses xtc-grps is the order in the traj.xtc determined by the order in conf.gro or in xtc-grps. For example, if we have in conf.gro SOL ION1 ION2 and xtc-grps = ION2 ION1 is the order in traj.xtc - ION1 then ION2 (as in conf.gro) or ION2 then ION1 (as in xtc-grps)

RE: [gmx-users] temperature too high with reaction field

Hi, This is normal. Reaction-field still uses a cut-off, which gives cut-off errors. To make the the error small you will need to reduce tau_t. Or use reaction-field-zero with a buffer region (computationally expensive). The real solution is to simply use PME. Berk > Date: Wed, 21 Jan 2009 17:5

[gmx-users] temperature too high with reaction field

Hi gmx users, I'm trying to simulate a water box filled with TIP3P water. With PME, everything seems OK. However, when I switch to reaction field electrostatics, the temperature in the output files is too high: 312K instead of 300K (the t_ref value for the whole system). Maybe there is somethin

[gmx-users] Re: Constant Velocity

Please read the manual. These questions are clearly answered there. On Wed, Jan 21, 2009 at 3:45 PM, avinash kumar wrote: > Dear Vitaly, > > Thank you for your reply regarding my query on giving a particular > group a constant velocity. However I request you to be more specific. > What will be

[gmx-users] Analysis of Pull-code results

Hello, I did a simulation of group pulling using umbrella mode in gromacs 4.0.2 Now I have pullf and pullx files and the trajectory itself. Pullf file show Force vs time dependence using KJ/(mol,mn) as Force units. How could I transform KJ/mol*nm to kj/mol units? Multiply each step by the length

Re: [gmx-users] MD simulating cyclic peptides including D-aminoacids

Hi, and thanks, David and Justin, for your answers. I thought there might be a problem with the dihedral angles like David suggested, too. However, what about using AMBER FF instead of OPLS ? Shouldn't make any difference, right ? Greetings, Joern Justin A. Lemkul wrote: Joern Lenz

[gmx-users] Quantitative output for g_mdmat ... a better way to list residue contacts

Dear Experts, I have a protein simulation from which I want to list residue-residue contacts. g_mdmat and xpm2ps provide a nice picture, but it would be nice to just have a list of contacts. Specifically ... which residues make contacts with which other residues. Is there a way to do this? Thank

Re: [gmx-users] Software Raid and low GROMACS performance

Hi Martin Martin Höfling escreveu: Am Dienstag, den 20.01.2009, 17:07 -0200 schrieb Alexandre Suman de Araujo: I have two machines with Intel Quad Core processors and Intel motherboards. In the first one I'm running Open Suse with normal partition scheme. In the second I'm running Ubuntu

[gmx-users] ResNumber in PDB2GMX

Hello users, i have just a simple question.. ..when I create a *.gro file starting from a PDB structure the numbers of residues start from 1 in the output file,even if in my initial protein the sequence start from another number.. Any suggestion to renumber correctly my output file? best r

[gmx-users] MD vs Scattering

Hi Can running MD to reproduce the data from scattering? If so, How? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before p

Re: [gmx-users] Is there any option to output interaction energy based on energy groups?

Liu Shiyong wrote: Hi, Is there any option to output total interaction energy (without *internal energy*) based on energy groups? If you can divide your system based on a few groups that are not covalently bound (i.e. no bonds, angles, dihedrals) then it will work easily for the shor

Re: [gmx-users] Bug in g_energy for calculating heat capacity?

bjorn.sat...@ift.uib.no wrote: On Sunday 21. December 2008 10.28.19 David van der Spoel wrote: Zhang Zhigang wrote: > Hi, all, > Actually I think others have also noticed this "bug": g_energy > often generate incorrect heat capacity. When I checked the source code > of gmx_energy.c, I fo