Dear All,
Is there any way to exclude non bonded parameters inbetween the same
topology molecules using GPUs? Are tabulated potentials supported by GPUs?
Please, advise
Steven
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Dear Gmx Users,
I wish to compare simulation of peptides in water with and without excluded
non-bonded parameters. My mdp file without exclusions:
; Run parameters
integrator = md; leap-frog integrator
nsteps = 5000; 100 ns
dt = 0.002 ; 2 fs
; Output control
Dear Users,
Would anyone suggest which option of g_cluster provides the number of
clusters gained over the simulation time? It would be an increasing plot
reaching plateau when the simulation is converged.
Please advise,
Steven
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,
That's very likely. GPU support in 5.0 is only for non-bonded interactions,
and CMAP is a bonded interaction. Of course, you could try it and see ;-)
Mark
On Mon, Sep 15, 2014 at 4:56 AM, Steven Neumann s.neuman...@gmail.com
wrote:
Please, advise.
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On Mon, Sep 15, 2014 at 7:46 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Mon, Sep 15, 2014 at 10:49 AM, Steven Neumann s.neuman...@gmail.com
wrote:
Thanks! Was it different in previous GMX versions? It is stated that
gromacs 4.6 does not support CMAP but nothing about 5.0 version
Please, advise.
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Dear Gmx Users,
I run US simulations between 2 nanotubes with attached proteins with
distance as a reaction coordinate. This is a coarse-grain simulation, both
tubes are placed across pbc so infinite in length. I have tabulated
potentials for both bonded and non-bonded interactions. I observed
ordering? (I am assuming you are using an explicit
solvent.)
Hope this helps,
Brian
On Tue, Aug 5, 2014 at 5:19 AM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I run US simulations between 2 nanotubes with attached proteins with
distance as a reaction coordinate
Dear Gmx Users,
Would someone suggest where I could find strucutre of POPC and POPS lipids
which once processed by pdb2gmx and Charmm36 would provide me a topology?
I found many stuctures but atoms are not matching and i have no clue which
one in the structure coresponds to which one in pdb.
Thanks a lot! How about POPS?
On Wed, Jul 30, 2014 at 12:26 PM, RINU KHATTRI nickname.mi...@gmail.com
wrote:
http://wcm.ucalgary.ca/tieleman/downloads
you can make the topology by command pdb2gmx
On Wed, Jul 30, 2014 at 8:23 AM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx
Dear Users,
My system includes 5 types of beads (coarse-grain) - 15 tabulated
potentials.
My mdp:
integrator = md
tinit= 0.0
dt = 0.01
nsteps = 140; 10 ns and 10 nm
nstcomm = 100
nstcalcenergy
Sorry I get the error with mdrun not grompp which works fine
On Fri, Jul 18, 2014 at 1:41 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Users,
My system includes 5 types of beads (coarse-grain) - 15 tabulated
potentials.
My mdp:
integrator = md
tinit
On Tue, Jun 3, 2014 at 8:25 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/2/14, 9:43 PM, Steven Neumann wrote:
Thanks but it will take some time to install 5.0 on the cluster. How about
[ angle_restraints_z ]? I could think of an atom in the protein to
restrain
along z axis (protein length
Dear Users,
I am trying to prevent rotation of my protein in recatngular box and I am
thinking about applying some position restraints with the dummy atoms. I
read some posts about this subject from 2003, 2006 but nothing recent. Is
there a gromacs tool to create a dummy atom a apply position
On Mon, Jun 2, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/2/14, 7:10 AM, Steven Neumann wrote:
Dear Users,
I am trying to prevent rotation of my protein in recatngular box and I am
thinking about applying some position restraints with the dummy atoms. I
read some posts
Lemkul jalem...@vt.edu wrote:
On 6/2/14, 9:15 PM, Steven Neumann wrote:
On Mon, Jun 2, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/2/14, 7:10 AM, Steven Neumann wrote:
Dear Users,
I am trying to prevent rotation of my protein in recatngular box and I
am
thinking about
Dear Gmx Users,
I am running REMD of a small protein in water. I have 36 temperatures.
After minimization I equilibrate each with nvt and npt ensemble. Then I
start REMD with -multidir. The mdp:
; Run parameters
integrator = md; leap-frog integrator
nsteps = 5000
dt =
What would you recommend then? Equilibrate with Berendsen barostat and
v-rescale thermostat?
On Mon, May 12, 2014 at 2:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/12/14, 3:58 AM, Steven Neumann wrote:
Dear Gmx Users,
I am running REMD of a small protein in water. I have 36
exchange is
not from the right ensemble, so all bets are off.
Mark
On May 13, 2014 4:01 AM, Steven Neumann s.neuman...@gmail.com wrote:
Or just to switch to NVT? I guess it would be less realistic if one wants
to study extract the most likely conformation...
On Tue, May 13, 2014 at 3:26
Dear Gmx Users, Dear Justin
I have noticed that in in our tutorial(s) in thew mdp option you suggesting
V-rescale thermostat and the Parinello-Rahman barostat. Is there any
particular reason for this choice? Would you please provide any reference
that is combinantion works well in comparison to
Thank you for this!
Steven
On Wed, Apr 9, 2014 at 2:14 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/9/14, 8:18 AM, Steven Neumann wrote:
Dear Gmx Users, Dear Justin
I have noticed that in in our tutorial(s) in thew mdp option you
suggesting
V-rescale thermostat and the Parinello
Thank you Justin. Indeed, the problem lies in maintaining the geometry... I
need to simplify the system for free energy calculations.
Steven
On Wed, Feb 19, 2014 at 1:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/18/14, 4:04 PM, Steven Neumann wrote:
Or maybe just 2 of them in the box
Dear User,
Can you please write me how to build a system of a protein (nonsymetric
obviously) and place it in the on the box edge so that one half is within
the unit cell and another one is copied across pbc on the other side? I
assume I will get the error doing manually...
please, advise.
PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/18/14, 11:19 AM, Steven Neumann wrote:
Dear User,
Can you please write me how to build a system of a protein (nonsymetric
obviously) and place it in the on the box edge so that one half is within
the unit cell and another one is copied across
PM, Steven Neumann s.neuman...@gmail.comwrote:
And the picture can be found here: http://speedy.sh/b73WM/Ssytem.png
On Tue, Feb 18, 2014 at 7:49 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thanks,
The picture is confidential so I will send it to you in the separate
msg. The distance
Dear Gmx Users,
I am trying to setup the system of nanotubes with attached polypeptides. I
wish to define the equlibrium distance (PMF minima) between them. However
in my system, I will have 6 of them in which one is in its quarter in the
rectangular each box edge copied across pbc. It is the
://gerrit.gromacs.org/#/c/2566/.
Mark
On Mon, Feb 17, 2014 at 2:27 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
Do you know whether it is possible to apply bonds/distance restraints or
constraints between two atom belonging to different moleculetypes?
Thanks,
Steven
Dear Users,
I am simulating a nanotube with bonds and LINCS = all-bonds. Because the
tube is bending I tried to apply bonds or LINCS constraints between atoms
lying oppositely within the circles (tube diameter) so I used just one to
check:
[ bonds ]
2485245117.465
And I get:
In your topology:
; Include Protein topology
#include protein.itp
; Include Position restraint file of ligand
#ifdef POSRES
#include posre_prot.itp
#endif
where posre_prot.itp
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original
.
Steven
On Wed, Feb 5, 2014 at 12:55 PM, Steven Neumann s.neuman...@gmail.comwrote:
Dear Users,
I am simulating a nanotube with bonds and LINCS = all-bonds. Because the
tube is bending I tried to apply bonds or LINCS constraints between atoms
lying oppositely within the circles (tube diameter
Thank you. Can you specify what does long mean? Is there any limit?
On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/5/14, 10:46 AM, Steven Neumann wrote:
Can you please advise? With large constraints it does not work... with [
distance_restraints ] it works
Maybe you know how do they keep nanotubes rigid then?
On Wed, Feb 5, 2014 at 3:58 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you. Can you specify what does long mean? Is there any limit?
On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/5/14, 10:46 AM
Thanks a lot!
Steven
On Wed, Feb 5, 2014 at 4:05 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/5/14, 11:05 AM, Steven Neumann wrote:
Maybe you know how do they keep nanotubes rigid then?
Nope, sorry.
-Justin
On Wed, Feb 5, 2014 at 3:58 PM, Steven Neumann s.neuman...@gmail.com
Dear Gromacs Users,
Can you please write me whther Gromacs 4.6 support tabulated potentials for
bonded and non-bonded interactions?
Steven
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Abraham mark.j.abra...@gmail.comwrote:
Yes, they get multiplied by parameters like charge, C6, C12 etc. Is that
the question you're asking? :-)
Mark
On Wed, Jan 15, 2014 at 8:02 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
Is there any way in Gromacs to scale
Dear Gmx Users,
Is there any way in Gromacs to scale tabulated potentials from
energygrp_table (non-bonded)?
Steven
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Dear Gmx Users,
I have my carbon nanotube (lenght z axis) with proteins attached to it. I
wish to collect RDF of given type of amino acids away from the surface in
two dimensions (xy). Z axis does not interest me. That would make a circle
then. My question: how to make a specific index group of
Dear Gmx Users,
I have built a coarse grained force field from scratch for my specific
protein. I wish to increase the time step, to see how much I can push it.
How can I assess it to see whether I did not go over given value as its
sure system specific. Would advise of some properties? Its a
, 2013 at 7:25 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you!
Steven
On Thu, Dec 5, 2013 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/5/13 12:57 PM, Steven Neumann wrote:
Thanks, I will apply harmonic bonds with whatever force constant then.
Would that speed up
:
On 12/4/13 11:48 AM, Steven Neumann wrote:
Dear Gmx Users,
My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON,
ACI, GLY and I want to create a topology. Is it possible to make one
residue of one [ moleculetype ] with this number of atoms so that:
[ moleculetype
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