[gmx-users] update .hdb file

​Hi I want to simulate a glycoprotein, I have defined a new residue with charmm36 inorder to update the .hdb file, I need to define the order of atoms that are conecting to atoms that is conecting to H atoms in my new residue but I dont exactly know about the standard format of showing atoms

Re: [gmx-users] EM replicates

Hi Gregory, Yes, these steps are deterministic. Think of where the randomization should come from. Sure, there is 'random' placement of ions in genion, but it has a default seed, resulting in deterministic random numbers :) Hope it helps, Tsjerk On Apr 9, 2016 00:33, "Gregory Poon"

[gmx-users] EM replicates

Hello all! I am wondering if the solvate, genion, and energy minimization (using steepest descent) procedures are deterministic. I have been performing replicate energy minimization of a duplex DNA structure, always starting from scratch (i.e., pdb2gmx) and using the same parameters in terms

[gmx-users] dual gpu setup questions

hey all, got a few questions for people with dual-gpu setups: - does anyone have tested and well performing explicit threading parameters for a typical GPU compute node with 2 CPU's + HT and dual GPU? The automatic settings for our hardware (2x8core cpu + HT & dual GPU) take 8MPI x 4OMP, which

Re: [gmx-users] desired usage of verlet-buffer-tolerance with charmm ff?

Dear Justin, Mark, and Szilárd: Thank you for all the help. I understand this a lot better now. My intended usage is REMD with PLUMED in gromacs 5.1.2 to do some replica exchange of the Hamiltonian. In this usage, the exchange attempts have to occur at steps when the neigborlist is updated.

[gmx-users] simulated annealing

Dear all, I would like to get a gel phase of a lipid bilayer system by simulated annealing (SA). I wonder in which step (NVT equilibration/velocity-generation, NPT equilibration, or MD run) I should apply SA. Best, Yao -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Fwd: Implementing GoIP parameters in OPLSAA

Dear GROMACS gremlins, I am trying in vain to implement the GoIP parameters for a gold-peptide interface in the OPLSAA ff. I began with just one kind of Au atom and now I want to put in two. When I execute gmx grompp -f em.mdp -c Au111.gro -p topol.top -o em.tpr I get this error Fatal

Re: [gmx-users] REMD of IDPs

Very good point from João. Always remember to check that your box length is big enough! === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

Re: [gmx-users] REMD of IDPs

One small remark to Micholas' email​: - Make sure the simulation box is big enough to allow the IDP to fully stretch without interacting with its periodic image(s). This is non-trivial if you build your system from a random coil. That's why I start from a fully stretched conformation instead of a

Re: [gmx-users] REMD of IDPs

Dear Yanhua, Converting a sequence into a structure is itself an "open" problem in computational biology/biophysics. There are ways to generate potential structures if you also happen to have some restraints from NMR or other experiments (small-angle scattering or CD-Spectra) noted in the

[gmx-users] select atoms of a particular zone, through trajectory

Dear users, I am trying to find out which water molecules are interacting with the ligand, in a protein-ligand simulated system and through the simulation time. Is there any way to find these molecules and extract a trajectory which includes these molecules plus my protein-ligand complex? best

Re: [gmx-users] desired usage of verlet-buffer-tolerance with charmm ff?

On Thu, Apr 7, 2016 at 9:55 PM, Christopher Neale wrote: > Dear users: > > Charmm mdp options are listed here: > http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM with the > following values: > > constraints = h-bonds > cutoff-scheme = Verlet >

Re: [gmx-users] Partial density versus time

Hi Tsjerk Your approach shows of course the appearance of the phase separation, but I necessarily need the time evolution of density of one component to see 'how' it reaches the equilibrium obtaining two difference mass fractions. Best regards. Best regards On Fri, Apr 8, 2016 at 12:34 PM,

Re: [gmx-users] Flat-bottom potential SEGFAULT

Hi, >From what I have observed so far this appears to be a cluster configuration >issue rather than a gromacs error. Thanks for your input. Kind regards, Erik On 29 Mar 2016, at 15:14, Erik Marklund > wrote: On 28 Mar 2016, at

Re: [gmx-users] semi-permeable wall in gromacs

Yes it worked. I appreciated to your help Justin. Thanks a lot. > On 07 Apr 2016, at 21:37, Justin Lemkul wrote: > > > > On 4/7/16 12:57 PM, gozde ergin wrote: >> Hi Justin, >> >> I just want to ask how is the r(nm) in posre.itp working? >> >> I would like to put

Re: [gmx-users] REMD of IDPs

​Dear Yanhua, To my knowledge (prior to gromacs 5.X at least), there​ are no gromacs tools able to turn a sequence into a PDB. The user must take care of that pre-processing on his/her own. I work with IDPs quite a lot, so what I can tell you is what I usually do. I take my fasta sequence and use