[gmx-users] Radius of Gyration

Dear all Does someone knows which equation is g_gyrate using to calculate the Rgx, Rgy, Rgz components of the Rg and which is the relation between them? I thougth that it was: Rg2=Rgx2+Rgy2+Rgz2, but at least for my results this is not the case. Thanks a lot Chrysostomos -- gmx-user

Re: [gmx-users] LJ cut-off distance

-users] LJ cut-off distance Προς: "Discussion list for GROMACS users" Ημερομηνία: Παρασκευή, 22 Οκτώβριος 2010, 18:27 On 23/10/2010 2:08 AM, C. Batistakis wrote: Dear Justin Actually, what I want to do

Re: [gmx-users] LJ cut-off distance

010, 17:51 C. Batistakis wrote: > Dear all > > I have a system of polymer chains between 2 substrates. The substrates are > FCC lattices consisting of Lennard-Jones particles.  > I would like to know if it’s possible to handle individually the cut-off > distances of the L

[gmx-users] LJ cut-off distance

Dear all I have a system of polymer chains between 2 substrates. The substrates are FCC lattices consisting of Lennard-Jones particles.   I would like to know if it’s possible to handle individually the cut-off distances of the LJ interactions in the system For example, I would to use one cu

Re: [gmx-users] g_gyrate

If you want to merge groups to get the radius of gyration over the union of those groups, then you need to use make_ndx on your previous .ndx file to generate such a group. Mark - Original Message - From: "C. Batistakis" Date: Tuesday, October 12, 2010 21:44 Subject: [gmx-users]

[gmx-users] g_gyrate

Dear all I have the following system. Substrate with 3696 particles and 4 polymer chains with 45 beads/chain.  After typing g_gyrate, I have the following option: Group 0 (  System) has  680 elements Group 1 ( ZZZ) has   500 elements Group 2 ( AAA) has    45 eleme

[gmx-users] Coarse-Grain: GROMACS bond information to VMD

Dear all I am trying to visuallize a coarse-grained model  I have created (long bond length!) with VMD. I saw the script coarse_grain.tcl but after many hours of trying I couldn't use it (I am a new user in VMD and I don't know how to source the script in VMD). Can anybody give some more "for

[gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx

Dear all According to the manual, pdb2gmx generates all the angles, pairs and dihedrals automatically in a polymer chain. Because I need nothing of them do you know any fast way to avoid this generation? The only think I found in the manual is to add [ exclusions ] in the .rtp file for whateve

Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

al Message ----- From: "C. Batistakis" Date: Wednesday, July 7, 2010 23:19 Subject: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 To: gromacs > Dear all   > I am trying to simulate Nitrile-Butadiene-Rubber, using the Gromos96 force field. Let the availability of

[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

Dear all   I am trying to simulate Nitrile-Butadiene-Rubber, using the Gromos96 force field. I have difficulties in finding the correct parameters from the bon.itp file , in order to define the polymer in the .rtp file.   Can someone suggest which parameters I shall choose in the followin