[gmx-users] the ligang topology

Dear, The topology for my ligand was created employing the server PRODRG 2.5 Beta. Now I change the charges to consistent with the GROMOS96,but I don't know the charges of -CF3 and C-Cl .Where can I find or can you tell me?Thanks! -- gmx-users mailing listgmx-users@gromacs.org http

Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Mark, I've used that dimensions in accordance to some literature where the same membrane-mimicking simulation were performed. I've tried to rise cutoffs and dicrease integration step but my system have been stil crashed during npt. I'm using pcoupl= Parrinello-Rahman wich I've found in

[gmx-users] BornSum: cudaMalloc in CUDAStream::Allocate failed out of memory

Hi! I'm trying to run a mdrun-gpu simulation on a 64-bit Ubuntu system. I'm using a 15GB GTX 580 NVIDIA GPU card with all the appropriate drivers and cuda toolkit. However, when I run the command: mdrun-gpu -s inpufile.tpr -c inputfile.gro -x outputfile.xtc -g outputfile.log -nice - 0 I get

[gmx-users] Water Shell Density

Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao -- gmx-users mailing list    gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] g_select -select

Hello, I am trying to make an dynamic index file of the hydration shell of my protein (hopefully using it with other gromacs tools). I am considering up to 10A from protein as the distance needed for my selection. I am using g_select with the following format: g_select -f traj.xtc -s traj.tpr -on

Re: [gmx-users] charmm27 in gromacs

In a nutshell, yes dihedral type 2 is for the IMPR charmm dihedrals and 9 is for the normal dihedrals. I think David or someone else added code to specifically support charmm dihedrals in this way. On 2012-02-14 09:32:37PM -0600, Tom wrote: > Dear Gmx Developer or Users, > > Can anyone explain wh

Re: [gmx-users] g_select -select

On 16/02/2012 6:15 AM, Paymon Pirzadeh wrote: Hello, I am trying to make an dynamic index file of the hydration shell of my protein (hopefully using it with other gromacs tools). I am considering up to 10A from protein as the distance needed for my selection. I am using g_select with the followin

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

On 16/02/2012 1:45 AM, James Starlight wrote: Mark, I've used that dimensions in accordance to some literature where the same membrane-mimicking simulation were performed. I've tried to rise cutoffs Don't, that breaks your model physics and makes it even more likely you will encounter prob

[gmx-users] how to interpret tilt from g_helixorient?

Hi all I'm also having trouble with g_helixorient and the data it is giving me. My desired end goal is to track the average tilt of a helix compared to the global Z-axis, but a change in the tilt of the helix over time to its reference structure (frame 0) will suffice. How exactly do I interpret

[gmx-users] in vacu simulation

Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0

Re: [gmx-users] in vacu simulation

Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw

Re: [gmx-users] Water Shell Density

Probably you can use g_rdf -surf to get the surface based g(r) for water molecules, since g(r) is the local_density divided by the average_density, then local_density=g(r)_surf*average_density, which is a function of distance from the surface. Jianguo From

Re: [gmx-users] in vacu simulation

On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist

Re: [gmx-users] the ligang topology

This paper has used united atoms for -CF3 and -CF2: Hiroaki et al. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study. J. Phys. Chem. B 2008, 112, 11305–11309. Another way is to use ATB to generate the topology, but I am not sure if it can deal with fluorine atom

[gmx-users] Re: charmm27 in gromacs

Got it. Thanks a lot for the help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the

Re: [gmx-users] in vacu simulation

On 15 February 2012 21:00, Mark Abraham wrote: > On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: > >> >> >> Juliette N. wrote: >> >>> Hi all, >>> >>> I am trying to run simulation in vaccum using the the changes shown >>> below to the usual mdp file. >>> pbc = no >>> >>> ;coulombtyp

[gmx-users] g_spatial index file

Hi, I used g_select to choose the hydration shell molecules of my protein from a trajectory of 15ns saved every 10ps (1500 frames). Now I want to feed the generated index file into g_spatial to calculate the SDF of solvent around my protein. However, when I feed this into the g_spatial, it lists 15

Re: [gmx-users] in vacu simulation

On 16/02/2012 2:08 PM, Juliette N. wrote: On 15 February 2012 21:00, Mark Abraham > wrote: On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the

Re: [gmx-users] g_spatial index file

On 16/02/2012 3:03 PM, Paymon Pirzadeh wrote: Hi, I used g_select to choose the hydration shell molecules of my protein from a trajectory of 15ns saved every 10ps (1500 frames). Now I want to feed the generated index file into g_spatial to calculate the SDF of solvent around my protein. However,

Re: [gmx-users] in vacu simulation

On 15 February 2012 23:05, Mark Abraham wrote: > On 16/02/2012 2:08 PM, Juliette N. wrote: > > > > On 15 February 2012 21:00, Mark Abraham wrote: > >> On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: >> >>> >>> >>> Juliette N. wrote: >>> Hi all, I am trying to run simulation in va

Re: [gmx-users] in vacu simulation

On 16/02/2012 3:14 PM, Juliette N. wrote: On 15 February 2012 23:05, Mark Abraham > wrote: On 16/02/2012 2:08 PM, Juliette N. wrote: On 15 February 2012 21:00, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 16/02/2012 12:22 PM, Just

Re: [gmx-users] in vacu simulation

Thanks. That was a new thing for me to learn. On 15 February 2012 23:19, Mark Abraham wrote: > On 16/02/2012 3:14 PM, Juliette N. wrote: > > > > On 15 February 2012 23:05, Mark Abraham wrote: > >> On 16/02/2012 2:08 PM, Juliette N. wrote: >> >> >> >> On 15 February 2012 21:00, Mark Abraham

[gmx-users] Placing ions in the specified positions

Dear Gromacs users! I've constructed my biphastic system with the water-ccl4-water layers where in the ccl4 layer I've placed my membrane protein. Now I'd like to place addition 5 Cl ions to the bottow leafleat of water to mimick the 'positive-inside rule' (my protein consist of 5 Lys) of the me

Re: [gmx-users] Placing ions in the specified positions

On 16/02/2012 6:13 PM, James Starlight wrote: Dear Gromacs users! I've constructed my biphastic system with the water-ccl4-water layers where in the ccl4 layer I've placed my membrane protein. Now I'd like to place addition 5 Cl ions to the bottow leafleat of water to mimick the 'positive-i