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
nst
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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Thanks. I will compare it.
On Mon, Sep 15, 2014 at 8:08 PM, Steven Neumann
wrote:
>
>
> On Mon, Sep 15, 2014 at 7:46 PM, Mark Abraham
> wrote:
>
>> On Mon, Sep 15, 2014 at 10:49 AM, Steven Neumann
>> wrote:
>>
>> > Thanks! Was it different i
On Mon, Sep 15, 2014 at 7:46 PM, Mark Abraham
wrote:
> On Mon, Sep 15, 2014 at 10:49 AM, Steven Neumann
> 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 that this
> >
at'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
> wrote:
>
> > Please, advise.
> > --
> > G
Please, advise.
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see whether your system
> shows unphysical 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
> wrote:
>
> > Dear Gmx Users,
> >
> > I run US simulations
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 tha
Thanks a lot! How about POPS?
On Wed, Jul 30, 2014 at 12:26 PM, RINU KHATTRI
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
> wrote:
>
> > Dear Gmx Users,
&g
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.
Plea
Sorry I get the error with mdrun not grompp which works fine
On Fri, Jul 18, 2014 at 1:41 PM, Steven Neumann
wrote:
> Dear Users,
>
> My system includes 5 types of beads (coarse-grain) - 15 tabulated
> potentials.
>
> My mdp:
>
> integrator = md
> tin
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
If you use atoms which are the part of the protein being restraint with the
z axis you get artificial behaviour. If I use dummy atoms being a part of
the protein N and C domain it is not the case...
On Wed, Jun 4, 2014 at 8:20 PM, Justin Lemkul wrote:
>
>
> On 6/3/14, 10:14 PM, Steve
Tue, Jun 3, 2014 at 8:25 PM, Justin Lemkul 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
>>
Lemkul wrote:
>
>
> On 6/2/14, 9:15 PM, Steven Neumann wrote:
>
>> On Mon, Jun 2, 2014 at 8:06 PM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 6/2/14, 7:10 AM, Steven Neumann wrote:
>>>
>>> Dear Users,
>>>>
>&
The version provided does not support GPUs... Is there any version with
rotational restraints implemented?
On Tue, Jun 3, 2014 at 9:15 AM, Steven Neumann
wrote:
>
>
>
> On Mon, Jun 2, 2014 at 8:06 PM, Justin Lemkul wrote:
>
>>
>>
>> On 6/2/14, 7:10 AM, Steven
On Mon, Jun 2, 2014 at 8:06 PM, Justin Lemkul 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 t
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 rest
May 14, 2014 at 3:50 AM, Steven Neumann >wrote:
>
> > Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no
> > crashes observed.
> >
> >
> > On Tue, May 13, 2014 at 2:08 PM, Mark Abraham > >wrote:
> >
> > > On May 13,
Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no
crashes observed.
On Tue, May 13, 2014 at 2:08 PM, Mark Abraham wrote:
> On May 13, 2014 7:21 AM, "Steven Neumann" wrote:
> >
> > Thanks a lot! So which combination of thermostat/barostat w
e is
> not from the right ensemble, so all bets are off.
>
> Mark
> On May 13, 2014 4:01 AM, "Steven Neumann" wrote:
>
> > Or just to switch to NVT? I guess it would be less realistic if one wants
> > to study extract the most likely conformation...
> &g
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 AM, Steven Neumann wrote:
> What would you recommend then? Equilibrate with Berendsen barostat and
> v-rescale thermostat?
>
>
>
What would you recommend then? Equilibrate with Berendsen barostat and
v-rescale thermostat?
On Mon, May 12, 2014 at 2:01 PM, Justin Lemkul wrote:
>
>
> On 5/12/14, 3:58 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> I am running REMD of a small protein in
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 =
Thank you for this!
Steven
On Wed, Apr 9, 2014 at 2:14 PM, Justin Lemkul 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
>&
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 ot
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 wrote:
>
>
> On 2/18/14, 4:04 PM, Steven Neumann wrote:
>
>> Or maybe just 2 of them i
PM, Steven Neumann wrote:
>
> And the picture can be found here: http://speedy.sh/b73WM/Ssytem.png
>
>
> On Tue, Feb 18, 2014 at 7:49 PM, Steven Neumann wrote:
>
>> Thanks,
>>
>> The picture is confidential so I will send it to you in the separate
>> msg.
what I mean? Or maybe build something easier...they all matter and will
have influence on the distance... hence no clue which one of them apply
with harmonic potential...
Steven
On Tue, Feb 18, 2014 at 7:16 PM, Justin Lemkul wrote:
>
>
> On 2/18/14, 1:37 PM, Steven Neumann wrote:
>
PM, Justin Lemkul 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
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.
Steve
omposition.
>
>
> Dr. Vitaly V. Chaban
>
>
>
> On Mon, Feb 17, 2014 at 9:38 AM, Steven Neumann
> wrote:
> > Dear Gmx Users,
> >
> > I am trying to setup the system of nanotubes with attached polypeptides.
> I
> > wish to define the equlibrium distance (P
cs.org/#/c/2566/.
>
> Mark
>
>
> On Mon, Feb 17, 2014 at 2:27 PM, Steven Neumann >wrote:
>
> > Dear Gmx Users,
> >
> > Do you know whether it is possible to apply bonds/distance restraints or
> > constraints between two atom belonging to different moleculety
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
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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 only
the size of your system and how much parallelism you want to
> use. See manual section on DD.
>
> Mark
>
>
> On Wed, Feb 5, 2014 at 4:58 PM, Steven Neumann >wrote:
>
> > Thank you. Can you specify what does long mean? Is there any limit?
> >
> >
> > O
Thanks a lot!
Steven
On Wed, Feb 5, 2014 at 4:05 PM, Justin Lemkul 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,
Maybe you know how do they keep nanotubes rigid then?
On Wed, Feb 5, 2014 at 3:58 PM, Steven Neumann wrote:
> Thank you. Can you specify what does long mean? Is there any limit?
>
>
> On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul wrote:
>
>>
>>
>> On 2/5/1
Thank you. Can you specify what does long mean? Is there any limit?
On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul wrote:
>
>
> On 2/5/14, 10:46 AM, Steven Neumann wrote:
>
>> Can you please advise? With large constraints it does not work... with [
>> distance_restra
.
Steven
On Wed, Feb 5, 2014 at 12:55 PM, Steven Neumann wrote:
> 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)
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 origin
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:
Dear Gmx Users,
I have 5 types of atoms which create a shape of the nonotube. 5 types of
beads correspond to future appliaction to which I will attach protein. I
wish the nanotube to be rigid and move in XY directions only. I created
bonds between all of them with app. b0=0.34 nm and a force const
Dear Gmx Users,
I have a tube made of atoms connected in lines:
Picture here: http://speedy.sh/BTRHx/tube.png
The edges of the tube are on the box edges with pbc - tube is infinite in
lenght then. I wish this tube to move only in XY directions so I froze the
Z coordinate using freezedim and free
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 wrote:
> 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 >wrote:
>
> > Dear Gmx Users,
> >
> > Is there any
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 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 rand
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 th
d84201000-2b2d84202000 ---p 2b2d84201000 00:00 0
> >> > 2b2d84202000-2b2d84402000 rwxp 2b2d84202000 00:00 0
> >> > 2b2d84402000-2b2d84403000 ---p 2b2d84402000 00:00 0
> >> > 2b2d84403000-2b2d84603000 rwxp 2b2d84403000 00:00 0
> >> > 2b2d88
> > 2b2da6bdf000-2b2da6cb4000 rwxp 2b2da6bdf000 00:00 0
> > 2b2da6d6d000-2b2da6ed rwxp 2b2da6d6d000 00:00 0
> > 2b2da6f0a000-2b2da7217000 rwxp 2b2da6f0a000 00:00 0
> > 2b2da7242000-2b2da76f9000 rwxp 2b2da7242000 00:00 0
> > 2b2da7708000-2b2da7987000 rwxp 2b2da7708000 00:00 0
[vdso]
ff60-ffe0 ---p 00:00 0
[vsyscall]
Abort
simulation is aborted. Would you please advise?
Steven
On Fri, Dec 6, 2013 at 9:39 AM, Steven Neumann wrote:
> I used bonds but with [ exclusions ] of 2516 atoms:
> 1 2 3. 2516
> 2 3 4 .2516
> ...
Thu, Dec 5, 2013 at 7:25 PM, Steven Neumann wrote:
> Thank you!
>
> Steven
>
>
> On Thu, Dec 5, 2013 at 6:03 PM, Justin Lemkul wrote:
>
>>
>>
>> On 12/5/13 12:57 PM, Steven Neumann wrote:
>>
>>> Thanks, I will apply harmonic bonds with whatever f
Thank you!
Steven
On Thu, Dec 5, 2013 at 6:03 PM, Justin Lemkul 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 the performance with all exclusions and bonds?
wrote:
>
>
> On 12/5/13 11:50 AM, Steven Neumann wrote:
>
>> Thanks I did it. However I got an error:
>>
>> Invalid order for directive exclusions
>>
>> My topology:
>>
>> [ defaults ]
>> ; nbfunccomb-rulegen-pairsfudgeLJfu
type resnr residue atom cgnr charge mass
typeBchargeB massB
; residue 1 TUB rtp TUB q 0.0
.
[ exclusions ]
.
I do not have any bonds dihedrals or angles...
would you advise?
Steven
On Thu, Dec 5, 2013 at 3:37 PM, Justin Lemkul wrote:
>
>
> On 12/
I found sth like this:
#!/usr/bin/python
# -*- coding: ISO-8859-1 -*-
#---#
# Function: Echo an exclusions list for Gromacs.
#
# Usage: exclusions.py [options] #-of-beads
#
# Help: run exclusions.py --help
#
# Author: Martti L
5/13 9:48 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> How can I apply exclusions of non-bonded parameters within my
>> [moleculetype] - I the positions of this molecule is restrained so all
>> non-bonded should be excluded. Would that need [ exclusions ]
Dear Gmx Users,
How can I apply exclusions of non-bonded parameters within my
[moleculetype] - I the positions of this molecule is restrained so all
non-bonded should be excluded. Would that need [ exclusions ] or
energy-monitor group can be applied?
what shall i specify
energy-monitor group = TUB
?
Steven
On Thu, Dec 5, 2013 at 1:41 PM, Steven Neumann wrote:
> Thank you
>
>
> On Thu, Dec 5, 2013 at 1:25 PM, Justin Lemkul wrote:
>
>>
>>
>> On 12/5/13 5:18 AM, Steven Neumann wrote:
>>
>>> I have not tried as wish to know before loosing time on ma
Thank you
On Thu, Dec 5, 2013 at 1:25 PM, Justin Lemkul wrote:
>
>
> On 12/5/13 5:18 AM, Steven Neumann wrote:
>
>> I have not tried as wish to know before loosing time on making the
>> topology. So each atom column needs letters - whats the maximum number of
>>
; 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 num
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 ]
; Namenrexcl
MOL3
[ atoms ]
;
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