[gmx-users] ligand parameterization for amber port in gmx

Dear people, I have parameterized a ligand with one phosphate and one pyrophospate group using antechamber with AM1-BCC charges and the GAFF forcefield. Amber files were converted to gmx files (*.itp/*.top and *.gro) with the amb2gmx conversion tool (http://www.alchemistry.org/wiki/index.php/Free_

[gmx-users] density and CG MARTINI force field

Dear people, I am trying to use the MARTINI CG force field from Marrink et al. for a 100 residue protein in water. I use the tools from the Marrink website (http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the necessary gro and itp files. For solvation of my protein I u

[gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial

hello, looking at the mdp`s in the above named tutorial, one sees that in em, pr, md the rvdw (1.4 nm) is always bigger than the rcoulomb (1.0 nm). given that electrostatic interactions have a longer range than lennard-jones potentials i do not understand this choice. thanks for any help. best

Re: [gmx-users] g_energy sum

i, > > > >If you haven't done anything special such as concatenating or cutting > the > >energy file in parts after the simulation, I'd say it looks like a bug. > >Please create an entry at bugzilla.gromacs.org , upload the tpr, and > we'll >

Re: [gmx-users] g_energy sum

ometimes it helps to read the mail. Mea culpa - forget my previous > answer, this is something else. > > It could simply be a bug in g_energy; which version are you using, > and what do you get if you remove "-b 2000" (i.e. include all steps)? > > Cheers, >

[gmx-users] g_energy sum

hello, when i calculate energies with g_energy -f (ener.edr) -b 2000 -sum -o (energy.xvg) e.g. i get this average in the log: Statistics over 101 steps [ 2000. thru 4000. ps ], 1 data sets Energy Average RMSD Fluct. Drift Tot-Drift

Re: [gmx-users] electrostatic and vdw energies from snapshots

from snapshots > Hi Merc, > > Why not resample your trajectory with a lower time resolution (i.e. > extracting snapshots) and only -rerun the resampled trajectory? Sounds > less time consuming than minimizing a number of snapshots. > > Cheers, > > Tsjerk > > O

[gmx-users] electrostatic and vdw energies from snapshots

hello, i would like to calculate the vdw and electrostatic energies for a part of my system that was not included in the energy groups during md. as a rerun would be too time consuming, i thought of taking snapshots from the md run, minimising those with the part of interest included in the ene

[gmx-users] positive 1-4 energy sum

hello, below are energies calculated for a 10 ns run. the sum of the 1-4 terms should not be positive, i think. does anyone know what could be the problem? i use these parameters: rlist= 0.9 coulombtype = PME rcoulomb = 0.9 rvdw

Re: [gmx-users] setup problem

Datum: Wed, 07 Mar 2007 11:20:22 +1100 Von: Mark Abraham <[EMAIL PROTECTED]> An: Discussion list for GROMACS users CC: Betreff: Re: [gmx-users] setup problem > merc mertens wrote: > > hello, > > > > i have got a problem with my simulation setup. i prepare a prot

[gmx-users] setup problem

hello, i have got a problem with my simulation setup. i prepare a protein with two ligands in a dodecahedral box. after the setup the ligands are situated in the active site of the protein all right. when i look at the structure after em one of the ligands is now outside the protein in the solv

Re: [gmx-users] invalid order of directive moleule type

if i were you, i would rather adapt my pdb file to an existing forcefield as ffgmx, than trying to generate a new forcefield that fits to your pdb with prodrug. the first option seems much easier to me. what i mean is, if you change the names of you FAD atoms to the ones you see in the *rtp they

Re: [gmx-users] Pdb for urea crystal

hello, your gro contains 8 urea molecules and your top only one. you should change the line " UREA 1" in your "[ molecules ]"-section to " UREA 8". merc Original-Nachricht Datum: Wed, 1 Nov 2006 17:46:59 +0800 Von: "Sivashangari Gnanasambandam" <[EMA

[gmx-users] g_hbond

hello, after using g_hbond to generate an *.xpm file one sees in the *.xpm file the following: "y-label: "Hydrogen Bond Index"" and the y-axis ranges between 0 and 163. if i look in the additionally generated hbbond.ndx file, i see at the bottom of it the group "[ hbonds_* ]". i assumed that th

Re: [gmx-users] protein in bilayer

this might help as well. http://www.dddc.ac.cn/embo04/practicals/9_16.htm#membraneproteinsinsertion Original-Nachricht Datum: Wed, 23 Aug 2006 14:31:35 +0300 Von: Itamar Kass <[EMAIL PROTECTED]> An: Discussion list for GROMACS users Betreff: Re: [gmx-users] protein in bilayer

[gmx-users] norleucine topology

dear list, to get a topology for norleucine i combined parameters from LEU (N,CA,CB, plus H´s, C, O) and MET (CG, CE, plus H´s). to get CD and its H´s i took parameters from MET CG as well. finally i adjusted the charges of CG and CD to get a residue topology with zero charge. can it be that ea

[gmx-users] REMD

hello, i am still trying to figure out how demultiplexing with trjcat (version 3.3.1) works. i produced 3 trajectories, each containing only one frame: e.g. traj0.xtc frame 0: natoms= 14670 step= 500 time= 1 prec= 1000 box (3x3): box[0]={ 8.47401e+00, 0

Re: Re: [gmx-users] REMD

> > the "time" stamps correspond to the first column in remd.xvg used for > trjcat. further, if *xtc is chosen as output in trjcat, for every single > frame the *xtc file contains the line: "not available: x", where there surely > is x in the single *trr files! > > > > e.g.: gmxdump_d -f traj0.tr

Re: Re: [gmx-users] REMD

> > remd.xvg was build like described above. output is only one trajectory, > containing only box information. > > > > additionally i tried: > > > > trjcat -f traj0.trr traj1.trr traj2.trr ... -o j0.xtc j1.xtc j2.xtc ... > -demux remd.xvg > > > > but from that i got only one trajectory as outpu

Re: Re: [gmx-users] REMD

> > > >so, if i observe in md.log an exchange like: > >"Repl ex 012 x 3" for e.g. time step 1 > >that would convert into: > >"1 0 1 3 2" > >for remd.xvg. is that correct? > >the problem is, if i do something like this for the entire time scale > trjcat only outputs the simulat

Re: [gmx-users] REMD

> you do need this option (-demux) and the xvg file should hold N+1 columns > containing the correct permutation of replicas, e.g. > > time repl 0 1 2 3 ... > 0 0 1 2 3 > 1 1 0 2 3 > 2 1 2 0 3 > > and so on so, if i observe in md.log an exchange like: "Repl ex 0

Re: Re: [gmx-users] REMD

hm, i want to produce one continuous trajectory from several trajectories, that are output from a REMD run. i could not find much information about this matter, but from what i read i gathered that one needs to reorder all the trajectories into a new one using the demux option in trjcat. as far

[gmx-users] REMD

Hello, at the end of a REMD run in gromacs I have as many trajectories as replicas used for simulation. To produce one continuous trajectory trjcat was recommended in a previous message. Since it neither makes sense to simply concatenate all trajectories nor can one sort them by time, I suspect