hi all freind
what is vdwtype in mdp file for LIE method in free energy calculation?
best regard
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
Dear Gmx Users,
I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.
I pulled my molecule away and two ions were also detached from the protein
surface being
On 2013-07-31 07:20, bipin singh wrote:
Hello All,
I was trying to do clustering on my MD trajectory using gromos method under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less
Thanks for the reply Prof. David. But in the output it shows that The RMSD
ranges from 0.0602553 to 0.411066 nm; this is the point of confusion to
me. So I think it should write the snapshots having RMSD greater than 0.3nm
(cutoff) to another cluster.
On Wed, Jul 31, 2013 at 12:59 PM, David van
What does your background reading suggest is a good choice for VDW type?
Mark
On Wed, Jul 31, 2013 at 9:18 AM, Mahboobeh Eslami
mahboobeh.esl...@yahoo.com wrote:
hi all freind
what is vdwtype in mdp file for LIE method in free energy calculation?
best regard
--
gmx-users mailing list
On 2013-07-31 09:45, bipin singh wrote:
Thanks for the reply Prof. David. But in the output it shows that The RMSD
ranges from 0.0602553 to 0.411066 nm; this is the point of confusion to
me. So I think it should write the snapshots having RMSD greater than 0.3nm
(cutoff) to another cluster.
I
Hi Bipin,
If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD 0.3 nm, they'll
end up in the same cluster.
Cheers,
Tsjerk
On Wed, Jul 31, 2013 at 9:45 AM, bipin singh bipinel...@gmail.com wrote:
Thanks for the reply Prof. David. But in the output it shows that The RMSD
ranges from
Now got the point. Thank you Tsjerk Sir and Prof. David for the help.
On Wed, Jul 31, 2013 at 1:42 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Bipin,
If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD 0.3 nm, they'll
end up in the same cluster.
Cheers,
Tsjerk
On Wed, Jul
Dear Users,
I am looking the way to extract the probability density of the C5-C6.
I will be very grateful to receive an indication on how to monitor it.
Best regards
Collins
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search
will get the PMF profile for my
ligand binding or ligand and two ions binding?
It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation?
Hello,
I have a problem and although I've read almost everything the internet could
offer on how differently people have approached this problem, mine hasn't
been solved yet.
Basically, I am trying to mix 2 different proteins in one box and after
doing my grompp to neutralise the system, I get
They do not dissociate...Are you sure? My mdp specifies only ligand as a
pull_group1. I think it would change having ions in this group included.
On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote:
will get the PMF profile for my
ligand binding or ligand and two ions
But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would Justin
please comment on this?
On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.comwrote:
They do not dissociate...Are you sure? My
Hi everyone
How can we have an error estimation for Gibbs binding free energy when
I do umbrella sampling and PMF profile?
Actually I did an umbrella sampling for protein and ligand complex and
I have a PMF profile now but I do not know how much is my error!
Thanks in advance for any
On 7/31/13 3:59 AM, Mark Abraham wrote:
What does your background reading suggest is a good choice for VDW type?
In addition, what does the chosen force field require?
-Justin
Mark
On Wed, Jul 31, 2013 at 9:18 AM, Mahboobeh Eslami
mahboobeh.esl...@yahoo.com wrote:
hi all freind
what is
On 7/31/13 6:04 AM, chinnu657 wrote:
Hello,
I have a problem and although I've read almost everything the internet could
offer on how differently people have approached this problem, mine hasn't
been solved yet.
Basically, I am trying to mix 2 different proteins in one box and after
doing my
On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
Hi everyone
How can we have an error estimation for Gibbs binding free energy when
I do umbrella sampling and PMF profile?
Actually I did an umbrella sampling for protein and ligand complex and
I have a PMF profile now but I do not know how much
Thank you for your reply Dr. Justin
On 7/31/13, Justin Lemkul jalem...@vt.edu wrote:
On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
Hi everyone
How can we have an error estimation for Gibbs binding free energy when
I do umbrella sampling and PMF profile?
Actually I did an umbrella
On 7/31/13 6:52 AM, Steven Neumann wrote:
But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would Justin
please comment on this?
I can offer you nothing more than a hand-waving explanation of what I
Thank you a lot!
On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/31/13 6:52 AM, Steven Neumann wrote:
But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would
Justin
please
I am do not want to choose different pulling conditions as I build a model
for specific force constant and pulling rate in given force filed. I think
restraining would help much more to then exclude the ions impact.
Steven
On Wed, Jul 31, 2013 at 12:49 PM, Steven Neumann
Sorry, still confused here:
I have a cell, that is same as residue, contains an inorganic crystal. But
since I am creating a surface I have bonds going across periodic boundary,
like Al and O shown on the pic? Can I still do it? How do I input it into
molecule.rtp?
Thank you,
V
On 7/31/13 8:57 AM, Valentina wrote:
Sorry, still confused here:
I have a cell, that is same as residue, contains an inorganic crystal. But
since I am creating a surface I have bonds going across periodic boundary,
like Al and O shown on the pic? Can I still do it? How do I input it into
perfect!
--
View this message in context:
http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010235.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
Thanks Justin. So, I've understood how to calculate the number of
coordinates. That in the topology file matches the amount I calculated (as
per how you just taught me).
I want to put 2 proteins in the same box. I did this by changing the
topology files of the respective proteins to itp. Then a
Dear Dr.Justin
I read that article, It was very helpful. Thanks a lot.
After using g_wham with bootstrapping options.
I have got an averaged PMF profile (like Fig.2C in that article) and
an standard deviation (like Fig.2D In that article) which obtained in
this way.
As you see, the standard
On Thu, Jul 25, 2013 at 5:55 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
That combo is supposed to generate a CMake warning.
I also get a warning during linking that some shared library will have
to provide some function (getpwuid?) at run time, but the binary is
static.
That warning
Hello
I am trying to calculate the RDF of water with water for a 10 ns MD of
pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default
-rdf option (atom).
The problem is that the integration of the RDF curve up to the first
minimum yields a zero value which is obviously not right
On Fri, Jul 19, 2013 at 6:59 PM, gigo g...@ibb.waw.pl wrote:
Hi!
On 2013-07-17 21:08, Mark Abraham wrote:
You tried ppn3 (with and without --loadbalance)?
I was testing on 8-replicas simulation.
1) Without --loadbalance and -np 8.
Excerpts from the script:
#PBS -l nodes=8:ppn=3
On 7/31/13 10:07 AM, chinnu657 wrote:
Thanks Justin. So, I've understood how to calculate the number of
coordinates. That in the topology file matches the amount I calculated (as
per how you just taught me).
I want to put 2 proteins in the same box. I did this by changing the
topology files
On 7/31/13 10:19 AM, Mohsen Ramezanpour wrote:
Dear Dr.Justin
I read that article, It was very helpful. Thanks a lot.
After using g_wham with bootstrapping options.
I have got an averaged PMF profile (like Fig.2C in that article) and
an standard deviation (like Fig.2D In that article) which
On 7/31/13 10:49 AM, George Patargias wrote:
Hello
I am trying to calculate the RDF of water with water for a 10 ns MD of
pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default
-rdf option (atom).
The problem is that the integration of the RDF curve up to the first
minimum
Hi Justin,
Oh, I see. I am going to paste my commands here.
pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce
pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce
editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0
editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0
cat conf1.gro conf2.gro
On 7/31/13 11:29 AM, chinnu657 wrote:
Hi Justin,
Oh, I see. I am going to paste my commands here.
pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce
pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce
editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0
editconf -f 2CDS_conf.gro -o
I did this with a small molecule and the ions were in the solvent, but associated with the ligand, and conversly if the site has a Mg or something etc...it wouldnt be restrained in the normal posres.itp unless you made one for them. It is in the end a matter of view, but I am assuming the change
renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro
topol_1AKI.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp
topol_2CDS.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp
I get the feeling you're not going to be able to see the
On 7/31/13 11:59 AM, chinnu657 wrote:
renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro
topol_1AKI.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp
topol_2CDS.itp
http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp
I get the feeling you're
Hi Justin
Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as
the the two groups!
So there must be a problem with the choice water-water or SOL-SOL for RDF
groups.
Many thanks!
On 7/31/13 10:49 AM, George Patargias wrote:
Hello
I am trying to calculate the RDF of
On 7/31/13 12:18 PM, George Patargias wrote:
Hi Justin
Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as
the the two groups!
So there must be a problem with the choice water-water or SOL-SOL for RDF
groups.
Indeed there would, because then (with -rdf atom) you're
Dear All,
How to calculate membrane curvature with function of time in gromacs? what
are the parameters that define curvature?
mean angle and distance and all ? can anybody help me to solve this problem
, because I am new to gromacs..:)
Thanks in advance,
--
--
gmx-users mailing list
Dear gmx-users,
I have run some tests (especially) for pure water, being able to achieve pretty
much perfect energy conservation in
NVE ensemble (with PME-switch and shifted VDW potential).
Then, just for the test, I continued to NVT ensemble by using previous .tpr and
.cpt files, but the
Hi all,
I'm running an expanded ensemble simulation using gromacs 4.6.3 and it
crashed with the error:
Fatal error:
Something wrong in choosing new lambda state with a Gibbs move -- probably
underflow in weight determination.
Denominator is: 0 1.002384e+00
idE
Thank you very much Justin. It's working fine now :)
Really appreciate it.
Chinnu
--
View this message in context:
http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010255.html
Sent from the GROMACS Users Forum mailing list archive at
I actually have another problem. When doing my grompp for nvt equilibration,
I egt the error, Topology include file posre.itp not found. In my topology
file I wrote this:
;Include the force field
#include oplsaa.ff/forcefield.itp
; Include chain topologies
#include topol_1AKI.itp
#include
On 7/31/13 2:48 PM, chinnu657 wrote:
I actually have another problem. When doing my grompp for nvt equilibration,
I egt the error, Topology include file posre.itp not found. In my topology
file I wrote this:
;Include the force field
#include oplsaa.ff/forcefield.itp
; Include chain
On 7/31/13 1:38 PM, Nikhil Agrawal wrote:
Dear All,
How to calculate membrane curvature with function of time in gromacs? what
are the parameters that define curvature?
mean angle and distance and all ? can anybody help me to solve this problem
, because I am new to gromacs..:)
Look
On Wed, Jul 31, 2013 at 7:47 PM, Janne Hirvi janne.hi...@uef.fi wrote:
Dear gmx-users,
I have run some tests (especially) for pure water, being able to achieve
pretty much perfect energy conservation in
NVE ensemble (with PME-switch and shifted VDW potential).
Great.
Then, just for the
Right, I've understood that now. I've altered all of that.
But somehow, the same error message still appears..
--
View this message in context:
http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010259.html
Sent from the GROMACS Users Forum
Hello,
I am performing a MD simulation on a small molecule in a bilayer. The
simulation seems to run smoothly but when i graph the energy i see large
changes in energy randomly throughout the run(see graph).
http://gromacs.5086.x6.nabble.com/file/n5010260/potential_12cc50.png
I have looked at
Thanks for your comments Mark,
If I understood correctly, you are saying, that maybe linear drift in
Conserved En. could indicate conservation of
that quantity, which we actually should be interested.
However, I made meanwhile some additional calculations and noticed that drift
in Conserved
On 7/31/13 3:10 PM, chinnu657 wrote:
Right, I've understood that now. I've altered all of that.
But somehow, the same error message still appears..
Without the command issued, exact error message (copied and pasted from the
terminal), and relevant topology snippet, there's nothing anyone
On 7/31/13 3:38 PM, Brad Van Oosten wrote:
Hello,
I am performing a MD simulation on a small molecule in a bilayer. The
simulation seems to run smoothly but when i graph the energy i see large
changes in energy randomly throughout the run(see graph).
Dear all,
I am looking how I can extract the interaction energy between specific
residue in a set of residues.
example:
I have DT and DA residues, I would like to plot only the energy of the DT.
I can extract the DT with the index file, But I am missing information on
how to plot the energy
Hi Tomas,
I am sorry to come with this further problem of gromacs.
I would like to plot an interaction energy between DT without include DA.
But I do not know how to ask make g_energy read my index file. Furthermore,
I was interested of the distance between C5-C6 in adjacent DT. But I do not
On 7/31/13 4:20 PM, Collins Nganou wrote:
Dear all,
I am looking how I can extract the interaction energy between specific
residue in a set of residues.
Nonbonded energy terms are decomposed using energygrps in the .mdp file along
with suitable index groups.
example:
I have DT and
looking at the first 2 peaks, they are created from single outlying points in
the trajectory. Visually, I can see no discernible difference between it and
the frame before/after with the higher energy.
--
View this message in context:
Hi Dejun-
The basic problem is that for this particular configuration, the
current state is the only state with nonzero weight. Note that the
state with the second highest weight has weight 10^-7. When it tries
to compare weights in single precision, it has a numerical overflow
and fails.
A few
Dear Gromacs users,
I am using gromacs 4.5.4 .
Is there any known issue/problem in running hamiltonian replica exchange
calculations or FEP with charm27.ff or amber forcefield in gromacs4.5.4 ? I
tried running an hamiltonian replica exchange using charmm27.ff by
interpolating A state and B
On 7/31/13 4:45 PM, Brad Van Oosten wrote:
looking at the first 2 peaks, they are created from single outlying points in
the trajectory. Visually, I can see no discernible difference between it and
the frame before/after with the higher energy.
To find the source, you'll probably have to
Dear All,
Can anyone guide me how to perform the 'potential energy scan' for a
dihedral of a small molecule in gromacs?
Regrads,
Tarak
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
60 matches
Mail list logo
