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
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 all,
I have a basic doubt. Is there any difference between the two processes
where
1) I concatenate the trajectories and do trjconv to remove PBC, which is a
default process
2) Do trjconv on all the xtc files separately and then concatenate them.
Thank you for your time
--
With Best Wishes
I do not think that I ever tried myself, but is seems all the same.
Why do you ask?
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote:
> Dear all,
> I have a basic doubt. Is there any difference between the two processes
> where
> 1) I concatenate the trajectories and do
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 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
Hi guys,
Is it possible to specify in the topol.top file preprocessor statements, so
that you can stop the simulation prematurely?
I pull two molecules together and I'd like to stop the simulation if the
center of mass distance of the molecules is less than xx nm.
Best,
grita
--
View this messa
Unlikely possible... But yeah, the feature might be handy.
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 4:20 PM, grita wrote:
> Hi guys,
>
> Is it possible to specify in the topol.top file preprocessor statements, so
> that you can stop the simulation prematurely?
>
> I pull two molecules toge
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
No, there's no way to do that. But you can monitor the output
trajectory file yourself, live.
Mark
On Thu, Sep 26, 2013 at 4:49 PM, Dr. Vitaly Chaban wrote:
> Unlikely possible... But yeah, the feature might be handy.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Thu, Sep 26, 2013 at 4:20 PM, grita wrote
Dear Sir,
Thanks for the quick reply.
I accidentally lost one of my raw .xtc files. But I have the noPBC xtc
file. So, when ever I extend my simulation, first I am removing PBC then
concatenating it with existing noPBC xtc file. Is it fine??
On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban wrot
Hi Venkat,
It depends on what you mean with "removing pbc".
Cheers,
Tsjerk
On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote:
Dear Sir,
Thanks for the quick reply.
I accidentally lost one of my raw .xtc files. But I have the noPBC xtc
file. So, when ever I extend my simulation, first I am removin
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
Hi
when calculating an energy contribution using g_energy, the units
specified in the plots, as well as in the output tables, are kJ/mol.
This happens even when the -nmol flag is missing (so nmol=1). On the
other hand, the energy units in gromacs are kJ/mol. So I guess that when
a term (a dihedral
Dear users,
For some analysis I require the 27 periodic images
of the system I ran the simulation for. Kindly let me
know how can it be written to a pdb file.
Thanking you
Regards
Kavya
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Pleas
Dear Tsjerk sir,
I used trjconv -pbc mol -ur compact options.
On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar wrote:
> Hi Venkat,
>
> It depends on what you mean with "removing pbc".
>
> Cheers,
>
> Tsjerk
>
> On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote:
>
> Dear Sir,
> Thanks for the qui
Hi Venkat,
These options are 'frame intrinsic' or 'history independent', unlike -pbc
nojump.
Cheers,
Tsjerk
On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote:
Dear Tsjerk sir,
I used trjconv -pbc mol -ur compact options.
On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar
wrote: > Hi Venkat, > >
Dear Users:
Has anyone successfully run the free energy tutorial at
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
?
I just tried it and I get a segmentation fault immediately (see output at the
end of this post).
I get a segfault with both 4.6.3 and
Hi Kavya,
genconf -nbox 3 3 3
Cheers,
Tsjerk
On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M wrote:
> Dear users,
>
> For some analysis I require the 27 periodic images
> of the system I ran the simulation for. Kindly let me
> know how can it be written to a pdb file.
>
> Thanking you
> Regard
Hi Ángel,
kJ per mol of system contained in the unit cell?
>
>
Exactly. As if whatever is in there is one 'molecule' (-nmol 1).
Adios!
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please searc
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 (
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
Dear GMX users:
Is OPLSAA forcefield data already available for POPC membranes. I am
interested in simulation of proteins in POPC membrane.
Thank you.
Best Regards
Karthi.
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the ar
I found the -multi version of that tutorial a bit temperamental...
Michael Shirts suggested that double precision is more reliable for
expanded ensemble. Hopefully he can chime in in a day or two.
Mark
On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale
wrote:
> Dear Users:
>
> Has anyone success
Thank you Mark.
I actually found that it crashed wihout the -multi part (no hamiltonian
exchange).
The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl
ethanol.1.dhdl.xvg
If I use the double precision version, there is no segfault. That's a working
solution, but it is worrysome.
Just to be clear, is this the expanded ensemble version of the calculation?
On Thu, Sep 26, 2013 at 5:25 PM, Mark Abraham wrote:
> I found the -multi version of that tutorial a bit temperamental...
> Michael Shirts suggested that double precision is more reliable for
> expanded ensemble. Hopefull
My mistake I still get a segfault even when using double precision. (EM
doesn't help, nor does switching to Berendsen pressure coupling).
Note that I can stop the segfault when running at init-lambda-state = 0 if I
set:
couple-lambda0 = none
couple-lambda1 = none
inste
No, this is not the expanded ensemble version. It's the initial "Running the
calculation with Gromacs" section straight out of
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
I get the segfault with a single run (at any of the 9 individual lambda values)
I thought I had just managed to solve the issue :)
If you look at the soft core parameters, there are two types listed --
one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power
are more stable with single precision calculations.
I have changed the files on the website to make the
And with this change, single is running fine as well.
This was a known issue, but was only documented in the expanded.mdp
files, which was an oversight. After this, I switched so the default
is less likely to cause problems. Because of some theory improvements
developed in the group in free ener
Agreed, the following parameters do not segfault in single or double precision:
sc-alpha = 0.5
sc-power = 1
sc-r-power = 6
Same goes for http://bugzilla.gromacs.org/issues/1306
The following parameters give a segfault in single precision but are ok in
Sounds like we've resolved all the confusion. Thanks for prompt help
in making this clearer and better.
On Thu, Sep 26, 2013 at 7:01 PM, Christopher Neale
wrote:
> Agreed, the following parameters do not segfault in single or double
> precision:
> sc-alpha = 0.5
> sc-power
Dear Users:
I'm having difficulty running MBAR after some free energy calculations (MBAR
via alchemical-gromacs.py obtained from alchemistry.org).
The input options to alchemical-gromacs.py have obviously changed since the
site at
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_etha
Dear Karthi:
As far as I am aware, there is no OPLSAA lipid force field. I have used Berger
lipids with OPLSAA protein
( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing
a UA lipid with an AA protein
so be aware of possible problems arising out of that.
Charmm has pr
On 9/26/13 10:47 PM, Christopher Neale wrote:
Dear Karthi:
As far as I am aware, there is no OPLSAA lipid force field. I have used Berger
lipids with OPLSAA protein
( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing
a UA lipid with an AA protein
so be aware of pos
Hi, Chris-
The best place to file this issue is the SimTK pymbar page, rather
than alchemistry.org, since it's a pymbar problem.
We have collaborators that may have updated the pymbar.py recently.
I'll try to get this stabilized in the very near future.
Testing quickly, my best guess is that it'
Dear Gigo:
I've never used tip5p, but perhaps you could add some LJ terms to the opls_120
definition,
do your minimization, then remove the fake LJ term on opls_120 and run your MD?
If that doesn't work, then you might be able to minimize your system using
FLEXIBLE tip3p
water and then use a sc
Thank you Sir!
Regards
Kavya
On Fri, Sep 27, 2013 at 12:52 AM, Tsjerk Wassenaar wrote:
> Hi Kavya,
>
> genconf -nbox 3 3 3
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M wrote:
>
> > Dear users,
> >
> > For some analysis I require the 27 periodic images
> > of the s
Thanks for the quick reply sir.
So, does it mean I can apply "trjcat" on the processed xtc files???
On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar wrote:
> Hi Venkat,
>
> These options are 'frame intrinsic' or 'history independent', unlike -pbc
> nojump.
>
> Cheers,
>
> Tsjerk
>
> On Sep 26,
Yes.
Cheers,
Tsjerk
On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote:
> Thanks for the quick reply sir.
> So, does it mean I can apply "trjcat" on the processed xtc files???
>
>
> On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar >wrote:
>
> > Hi Venkat,
> >
> > These options are 'frame
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