Thank you!
Steven
On Thu, Oct 10, 2013 at 3:02 PM, Justin Lemkul wrote:
>
>
> On 10/10/13 10:01 AM, Steven Neumann wrote:
>
>> Thanks a lot. I will use position restraints then with a strong force
>> constant, no bonds and place the edge atoms within half of distance
>> between
>> them from th
On 10/10/13 10:01 AM, Steven Neumann wrote:
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance between
them from the box edge. Is that correct?
Seems reasonable. One way to find out...
-Justin
--
==
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance between
them from the box edge. Is that correct?
Steven
On Thu, Oct 10, 2013 at 2:56 PM, Justin Lemkul wrote:
>
>
> On 10/10/13 9:54 AM, Steven Neumann wrot
On 10/10/13 9:54 AM, Steven Neumann wrote:
Thank you. I do not have any explicit solvent in my system. I included the
solvent in nonbonded parameters so not even implicit.
Well, presumably you have other things in the system, otherwise you're
simulating an inert tube of non-interacting atom
On 10/10/13 9:53 AM, Steven Neumann wrote:
Thank you. Would both be equal in terms of gaining computational time?
No idea. You definitely would not gain anything from using the [nonbond_params]
approach. Maybe with exclusions.
-Justin
--
Thank you. I do not have any explicit solvent in my system. I included the
solvent in nonbonded parameters so not even implicit.
Steven
On Thu, Oct 10, 2013 at 2:47 PM, Justin Lemkul wrote:
>
>
> On 10/10/13 9:44 AM, Steven Neumann wrote:
>
>> Thanks. I will place them then within the distance
Thank you. Would both be equal in terms of gaining computational time?
Steven
On Thu, Oct 10, 2013 at 2:46 PM, Justin Lemkul wrote:
>
>
> On 10/10/13 9:39 AM, Steven Neumann wrote:
>
>> And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] -
>> is
>> there any gmx tool to excl
On 10/10/13 9:44 AM, Steven Neumann wrote:
Thanks. I will place them then within the distance from the box edge =
distance between atoms within the tube right? I can create bonds and use
harmonic spring constant like for backbone protein atoms...but whats the
point when they do not move anyway?
On 10/10/13 9:39 AM, Steven Neumann wrote:
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is
there any gmx tool to exclude interactions within the given molecule so 1
with all 1200, 2 with all 1200...etc... 1200 with all 1200?
No, but it's a simple script to write s
Thanks. I will place them then within the distance from the box edge =
distance between atoms within the tube right? I can create bonds and use
harmonic spring constant like for backbone protein atoms...but whats the
point when they do not move anyway? I am using NVT.
Steven
On Thu, Oct 10, 2013
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is
there any gmx tool to exclude interactions within the given molecule so 1
with all 1200, 2 with all 1200...etc... 1200 with all 1200?
Steven
On Thu, Oct 10, 2013 at 2:34 PM, Steven Neumann wrote:
> Thanks a lot. You the
On 10/10/13 9:34 AM, Steven Neumann wrote:
Thanks a lot. You the bond as a distance between atoms? I wish to avoid
bonds as they are not necessary...just position restraint. What would be
the force constant? I tried 1000 once without bonds and my atoms were
moving a bit...
If you don't have
Thanks a lot. You the bond as a distance between atoms? I wish to avoid
bonds as they are not necessary...just position restraint. What would be
the force constant? I tried 1000 once without bonds and my atoms were
moving a bit...
Steven
On Thu, Oct 10, 2013 at 2:28 PM, Justin Lemkul wrote:
>
On 10/10/13 9:21 AM, Steven Neumann wrote:
How about applying position restarints with a strong force constant? What
is less computationally expensive: position restrained, freezing the whole
molecule? The nanotube should be rigid... Shall I place the edged of the
You shouldn't see any real p
How about applying position restarints with a strong force constant? What
is less computationally expensive: position restrained, freezing the whole
molecule? The nanotube should be rigid... Shall I place the edged of the
tube on the box edge as well and use pbc=xyz and periodic molecules = yes?
T
On 9/26/13 10:19 AM, Dr. Vitaly Chaban wrote:
I am just curious why the system would explode without
"periodic_molecules = yes". If the PBC procedure is applied before
harmonic bond potential is calculated, than the opposite nanotube
atoms should be (already) seen as neighboring. This looks the
On 9/26/13 12:05 PM, Dr. Vitaly Chaban wrote:
Steven -
I would use a simple harmonic bond.
Note that either in the case of the distance restraint or harmonic interaction
approach, both the CNT and the molecule to which it is tethered need to be in
the same [moleculetype], so run pdb2gmx (
Steven -
I would use a simple harmonic bond.
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann wrote:
> Thank you for this. And also I wish to attach a chain to my nanotube so they
> will be both able to move together. Is that a matter of distance restraints
> between nanot
Thank you for this. And also I wish to attach a chain to my nanotube so
they will be both able to move together. Is that a matter of distance
restraints between nanotube atom and first atom of my chain or again -
LINCS? Both chain and nanotube are made of the same type of 8 type of
atoms. Please, a
I am just curious why the system would explode without
"periodic_molecules = yes". If the PBC procedure is applied before
harmonic bond potential is calculated, than the opposite nanotube
atoms should be (already) seen as neighboring. This looks the same as
the solvent molecule, one atom of which c
On 9/26/13 8:39 AM, Steven Neumann wrote:
Dear Gmx Users,
I have my carbon nanotube and I wish to make it infinite in lenght. Which
mdp options whall be used? pbc = xy and z is the infinite dimension?
another issue: Would you apply bonds between carbon atoms within the
nanotube or constraints
I think this is in topology, not in MDP. With PBC, you just specify
what happens to the particle after it crosses the edge of the box in
certain direction.
I have no preference regarding LINCS vs harmonic bonds.
You can also "freeze" only the rim atoms of the nanotube from both
ends and this will
Dear Gmx Users,
I have my carbon nanotube and I wish to make it infinite in lenght. Which
mdp options whall be used? pbc = xy and z is the infinite dimension?
another issue: Would you apply bonds between carbon atoms within the
nanotube or constraints using LINCS? Which of them is less computation
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