Re: [gmx-users] CG to Atomistic

Another option is to use the VMD CG Builder Tools Plugin: http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/ Check out the section "Reverse Previously RBCG Model Back To All-Atom". 2009/8/7 Edson Fauth Vargas Filho > Hi. > I would like to know how can I convert a coarse-grained PDB into atom

Re: [gmx-users] CG to Atomistic

Johnny, I have only used CG Builder to convert atomistic models to coarse-grained models. However, I think if you accurately specify your groups of atoms to CG beads in your .RCG file, the plugin should work just fine. It is also noted on the VMD website you *need* your original atomistic PDB in

Re: [gmx-users] Re: I need help for gromacs

Hi Veli, Try this: genion -s EM.tpr -o oution.gro -np -random Select "3" to replace the water molecules with ions. (Make sure you update your number of water molecules and ions in your topol.top file.) When you're learning Gromacs it's probably a good idea to consult tutorials online first. I

[gmx-users] Exotic metal species

Der all, I'd like to know if any has had experience in using GROMACS for modeling exotic metal species like Gadolinium(III) and Indium(III)? My system is actually an Indium(III) ion coupled to DTPA (diethylenetriaminepentaacetate), an octadentate ligand forms bonds with metals through three atom

Re: [gmx-users] Exotic metal species

, can I safely assume that charge transfer is not an issue for running simulations on In(III)-DTPA using another MD-based package like Gromacs? Thanks, Lili 2009/8/12 David van der Spoel > Lili Peng wrote: > >> Der all, >> >> I'd like to know if any has had ex

[gmx-users] Problem with running MD

Hi all, I am having a problem while running an MD simulation on a system of 11 identical molecules solvated in a 50nm X 50 nm X 50nm box with Na+ ions. I submit my job, and it starts to run successfully. However, after 2500ps, the xtc and trr files do not increase in size anymore, which I presu

Re: [gmx-users] Problem with running MD

hing seems alarming. Is there anything else I should look into to figure out what is causing my system to stall? Thanks, L 2009/8/20 Justin A. Lemkul > > > Lili Peng wrote: > >> Hi all, >> >> I am having a problem while running an MD simulation on a system of 11 >

[gmx-users] Using make_ndx

Hi everyone, I'm trying to figure out the right commands for make_ndx so to generate the correct index.ndx file for g_bond analysis. From my PDB file: ATOM 1 BN0 GGA X 1 107.255 17.133 66.368 1.00 0.00 P1 C ATOM 2 SC1 GGA X 1 110.304 14.942 66.116 1.00 0.00

[gmx-users] Determining surface charge of a molecule

Hi Gromacs users, Is there a way to determine the surface charge of a molecule solvated in a water box? I'm aware that g_density can be used to determine the electronic charge density across a box system and g_potential can be used to determine the electrostatic potential across the box. Is ther

Re: [gmx-users] Determining surface charge of a molecule

It's just the electrical charge on the surface of the molecule, at the interface between the molecule and solvent. 2009/9/1 Mark Abraham > Lili Peng wrote: > >> Hi Gromacs users, >> >> Is there a way to determine the surface charge of a molecule solvated in a