Hello:
I submitted MD simulation for two small peptides with Amber FF. I
calculated the average potential energy of the system:
peptide A: -9x10^4 kcal/mol
peptide B: -6X10^4 kcal/mol
it seems that peptide A is more stable than B.
However, if I extract each frame the peptide from MD simulat
Hi Qasim,
> On 12 Jan 2017, at 20:22, qasimp...@gmail.com wrote:
>
> Hi Carsten,
>
> I think I couldn't clearly explain the protocol that I follow. Sorry for
> that. Firstly, I do the EM, nvt (100 ps), npt (100 ps) and md (100 ns) steps
> for the equilibrium. In all those steps I use the below
Hi gromacs users,
I am using gromacs in windows 7, 64 bit.
When the following command was given,
gmx g_energy -f ener.part0001.edr -o vol.xvg
the error was
GROMACS: gmx, VERSION 5.1.1
Executable: /usr/local/gromacs/bin/gmx.exe
Data prefix: /usr/local/gromacs
Command line:
gmx
gmx energy should be the correct command.
> On 13 Jan 2017, at 10:53, Subashini .K wrote:
>
>
> Hi gromacs users,
>
>
> I am using gromacs in windows 7, 64 bit.
>
>
> When the following command was given,
>
>
> gmx g_energy -f ener.part0001.edr -o vol.xvg
>
>
>
> the error was
>
>
> G
Dear Gromacs Users,
We would like to introduce a recently published article on calculation
of relative free energies.
http://www.sciencedirect.com/science/article/pii/S0010465516303411
The article includes a decoupling analysis in which the partition
functions of the transformed molecules
Dear list subscribers,
we are very happy to announce that also this year, the traditional
Molecular Modelling Workshop in Erlangen takes place on
March, Monday 27th to Wednesday 29th, 2017.
Starting on Monday after lunch should allow to avoid travelling on
weekend keeping the expens
Hi,
I am trying to calculate PMFs for a number of protein-protein complexes, doing
pulling and Umbrella sampling mainly following the protocol found in Justins
tutorial.
In my case it feels like I should remove position restraints in the umbrella
sampling on the peptide that is kept stationary
Maybe you should visit the manual for your last questions.
In my paper I have also followed the Justin’s tutorial however I did not use
restraint because for my purpose it was unnecessary.
Justin used it because restraining one peptide makes the remaining four
peptides more stable.
> On 13 Jan
Hi,
Having low potential energy (whether in dynamical simulation or em) and
being (any kind of) stable are nearly unrelated concepts. There may be a
way to measure what you want, but so far I suspect you haven't worked out a
good way to describe what you want.
Further, unless your peptides are is
Hi Mark.
thanks a lot for your comments.
These two peptides are isomers.
I want to know which conformations is more favourable than the other
from the aspect of potential energy.
However, the system potential energy and the peptide potential energy
seems to be inconsistent with each oth
Do you have the same amount of molecules in each simulation?
Anders
On Fri, Jan 13, 2017 at 12:19 PM, Albert wrote:
> Hi Mark.
>
> thanks a lot for your comments.
>
> These two peptides are isomers.
>
> I want to know which conformations is more favourable than the other from
> the aspect of po
noprobably that's the reason?
On 01/13/2017 12:23 PM, Anders Støttrup Larsen wrote:
Do you have the same amount of molecules in each simulation?
Anders
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Dear Gromacs User,
I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:
*NOTE 1* [file topol.top]:
The largest charge group contains 11 atoms.
Since atoms only see each other when the cente
Hi,
On Fri, Jan 13, 2017 at 12:20 PM Albert wrote:
> Hi Mark.
>
> thanks a lot for your comments.
>
> These two peptides are isomers.
>
> I want to know which conformations is more favourable than the other
> from the aspect of potential energy.
>
But that doesn't tell anybody anything. A l
On 1/13/17 6:43 AM, Nivedita Rai wrote:
Dear Gromacs User,
I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:
*NOTE 1* [file topol.top]:
The largest charge group contains 11 atoms.
Si
On 1/12/17 11:20 PM, Mohsen Ramezanpour wrote:
On Thu, Jan 12, 2017 at 8:36 PM, Justin Lemkul wrote:
On 1/12/17 10:21 PM, Mohsen Ramezanpour wrote:
On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul wrote:
On 1/12/17 7:47 PM, Mohsen Ramezanpour wrote:
On Thu, Jan 12, 2017 at 4:24 PM, J
Hi,
I’m trying to extract a list of frames from a long trajectory:
gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc atom
-o conf_test.gro -sep
where frames.ndx contains the following:
[ frames ]
2 3 4 5 6 8 ...
Each frame is supposed to be separated by 10 ps, so that
Hi,
I was writing in thread in gmx-userlist. But suddenly the mail (entitled:
pulling protein-ligand complex) got stuck for moderator approval. After a
waiting for a while, it is still not being delivered to the list.
Any help would be nice !
--
Abhisek Mondal
*Research Fellow*
*Structural Bio
Hi,
Sadly there's nothing to be done except ignore the field or do multiple
passes. The history of trjconv is a large number of people adding features
convenient for their use case, and not knowing how it interacts with the
huge surface area of the set of all other features. So the person who
want
Hi,
I suggest you find ways to make it smaller, eg provide links to mdp files
on file sharing services, etc
Mark
On Fri, 13 Jan 2017 14:27 abhisek Mondal wrote:
> Hi,
> I was writing in thread in gmx-userlist. But suddenly the mail (entitled:
> pulling protein-ligand complex) got stuck for mod
Hi,
So for some reason, the frame numbers I list won't match the timestamps when I
use -fr. Is there a way to extract frames based on timestamps? The problem is,
I want to be reading the file only once (or a few times), as it is huge (~500
GB), so I can’t use -dump by calling trjconv hundreds o
On 13/01/17 14:41, Irem Altan wrote:
Hi,
So for some reason, the frame numbers I list won't match the timestamps when I
use -fr. Is there a way to extract frames based on timestamps? The problem is,
I want to be reading the file only once (or a few times), as it is huge (~500
GB), so I can’t
I need to sample with logarithmic time intervals.
On Jan 13, 2017, at 3:12 PM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>> wrote:
On 13/01/17 14:41, Irem Altan wrote:
Hi,
So for some reason, the frame numbers I list won't match the timestamps when I
use -fr. Is there a way to extract fra
On 1/13/17 9:15 AM, Irem Altan wrote:
I need to sample with logarithmic time intervals.
Use -b to speed up moving through the trajectory before dumping the desired time
frame, or split the massive trajectory into smaller, more manageable chunks that
you can loop over simultaneously.
-Jus
When I do that it still reads from the beginning, saying “skipping frame”. I’ll
divide the file in a few pieces and save all configurations. I’ll then cat the
configs that I want. This is the simplest thing I can think of.
> On Jan 13, 2017, at 3:17 PM, Justin Lemkul wrote:
>
>
>
> On 1/13/1
Dear Gromacs Users,
I am running gromacs 2016.1 on a server. After the simulation, I want to
obtain the center of mass rdf using the following command:
gmx_mpi rdf -f prod.xtc -s prod.tpr -o rdf.xvg -com -rdf mol_com
However I got an error:
Program: gmx rdf, version 2016.1
Source file: src/
Hi,
That functionality has been re-implemented, and is now invoked differently.
See
http://manual.gromacs.org/documentation/2016.1/user-guide/cmdline.html#id1
Mark
On Fri, Jan 13, 2017 at 6:18 PM Boning Wu
wrote:
> Dear Gromacs Users,
>
> I am running gromacs 2016.1 on a server. After the simu
Thanks. interesting!
So, for now, lets focus on one of those dihedrals which has another
equivalent.
If I do PES on a rotatable bond in one ethyl, the other equivalent
rotatable bond in other ethyl will be free to move. If I understood
correctly, you meant it does not matter and I can do PES with o
On 1/13/17 3:26 PM, Mohsen Ramezanpour wrote:
Thanks. interesting!
So, for now, lets focus on one of those dihedrals which has another
equivalent.
If I do PES on a rotatable bond in one ethyl, the other equivalent
rotatable bond in other ethyl will be free to move. If I understood
correctly, yo
Hi everyone,
I am pulling a water molecule into a bilayer using an absolute reference
(mdp file below). I have tried to adapt methodology in Justin Lemkul's
umbrella sampling tutorial, but I have encountered a couple issues:
1) The bilayer (already well-equilibrated) is either being pulled or
dri
Dear all,
Protein-ligand complex MD simulation using Gromacs 5.1.4
Can you please tell me command for Number of Hydrogen bond plot? and
Other interactions between protein and ligand?
Regards,
Adarsh V. K.
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