[gmx-users] Density Deferences between spc216 and tip4p water models

Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540 atoms in 32885 residues Vol

[gmx-users] is there performance data for GROMACS on Blue Gene/L?

Does anybody have access to any performance data for GROMACS on a Blue Gene/L system? I'm putting together a proposal for some time on such a machine, and some moderately accurate costings would be nice. Mark ___ gmx-users mailing listgmx-users@gr

[gmx-users] Gel Phase in DMPC using Berger force field ?? -- Focus: naming convention

Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. I

[gmx-users] Range checking error

Dear Gromacs-Users, Is there anybody have met such problem before? I did NTP simulation for POPE system downloaded from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. It can run for even 10 ns with single precision GROMACS on many processors or with double precision GROMACS

[gmx-users] Re: Diagnosing an explosion

Apologies for replying to myself - maybe I can sharpen up some of my original questions below: Reply below > >> I am having a problem with my BD simulation either crashing with a Range >> error or locking up the mdrun process completely. >> >> I am running Gromacs 3.3.1 (must use this versi

[gmx-users] Is there any way to do r^3 distance dependence?

Hi, all, I know that Gromacs has the capability of restraining a molecule with r^6 distance dependence. Is there any way to do r^3 distance dependence? Best wishes, Art Roberts University of Washington Department of Medicinal Chemistry Seattle, WA 98195 ___

Re: [gmx-users] literature on GROMOS96 43b1 force field and vacuum simulations

On Wed, 12 Dec 2007 11:24:01 +0100 Carsten Baldauf <[EMAIL PROTECTED]> wrote: dear all// i am looking for literature describing the gromos 96 force fields, especially the vacuum force field 43b1. unfortunately i don't find much besides the gromos manual ... look for gromos force field you sh

Re: [gmx-users] Methanol SOL :Number of solventmolecules = 0

Stop the minimization at 100 steps and then equilibrate. If the problem persists check your topology. XAvier Dear Dr. Xavier Periole, Thank you for guiding me through. I could solve the problem of settin

Re: [gmx-users] pbc and tpr file

Hi, Thanks for your reply. The protein I simulated has 16 subunits. I checked the protein struture (no jump) in the tpr file and there are no contacts between each subunits. The protein structure in the fist frame of simulation seems ok, but has jumps. Two strucutres are very different and I do no

Re: [gmx-users] Methanol SOL :Number of solventmolecules = 0

Dear Dr. Xavier Periole, Thank you for guiding me through. I could solve the problem of setting up the system for minimization. However When started minimization run for 2000 steps with ste

[gmx-users] literature on GROMOS96 43b1 force field and vacuum simulations

dear all// i am looking for literature describing the gromos 96 force fields, especially the vacuum force field 43b1. unfortunately i don't find much besides the gromos manual ... do you have any suggestions/hints? thank you very much// carsten p.s.: just in case you would want to perform a md

[gmx-users] problem using makehole program

Dear All i started makehole program...but am facing problems setting the mdp parameters. when i gave mdrun command i get an error..that i cant make out: the command i gave is:- /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun -v -hole -holep hpgr.mdp -s dmpc_water_1ns.tpr -o cecmel311334_dmpc_hol

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

Dear Sir, I'm absolutely aware that gromacs uses nm for distance. The values should be 0.556 and 0.89. I used them only for reference purposes and I hope that this didn't cause any misanderstanding so as to point me to the manual. If this is the case of not understanding my questions, I deeply app

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

Dear all, For the gel-to-liquid crystalline phase transition in DPPC and DPPE there is a paper: Leekumjorn and Sum, BBA, 1768 (2007) 354-365 I've found it several month ago and I haven't red through it completely, but they used the Berger force field. Best, Zoltan Eric Jakobsson <[EMAIL PROTEC

Re: [gmx-users] asking for recommendations

Hi Michelle, What reasons do you have suggesting factors other than modelling limitations? Is there experimental data regarding the time scale of uncoiling? I would guess it would take longer than 20 ns. Also, you should consider that you're looking at a single molecule. The observation of uncoili

[gmx-users] asking for recommendations

Hi! I am a student currently using GROMACS (which I am new at) for a study on iota-carrageenan. The starting structures used are already in a double helix configuration. One file contains two ten-monomer iota-carrageenan chains coiled into a double helix; the other two files (differing only i

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

On Wed, 12 Dec 2007, Claus Valka wrote: Dear Sir, I would try to be more precise. example1 mdp file: rlist = (greater or equal to rvdw) vdw-type = Switch rvdw-switch=5.56 rvdw=8.9 are you aware that gromacs usues nm for distance? you can find the functional form of the shift/switch functi

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

Yes, this should be attempted. Perhaps the ultimate test of a force field is to nail a phase change. At 03:34 AM 12/12/2007, you wrote: Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challeng

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

Dear Sir, I would try to be more precise. example1 mdp file: rlist = (greater or equal to rvdw) vdw-type = Switch rvdw-switch=5.56 rvdw=8.9 Between the value 5.56 and 8.9 gromacs uses cubic spline? example2 mdp file: rlist=5.56 vdw-type = Cut-off rvdw-switch=0 (this value here should be irrele

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challenging...but yes, as you said, would be interesting... Cheers, Jochen Eric Jakobsson wrote: Several points: What is called the Berger forc

Re: [gmx-users] pbc and tpr file

Hi Tang, It doesn't hurt to check (i.e. you should check ;)) whether the .tpr file contains the protein "in one piece", if you want to use it as a reference structure for rmsd calculations. You can extract the coordinates from the .tpr file using editconf and then have a look. Actually, you should