On 5/10/2012 3:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much.
So, decreasing of box dimensions is not bad, if all thing process natural, yes?
The cause of my doubt was because of in the most of articles was said for example
we select box with dimensions 10nm that after
Dear Mark,
Yes, you're right. Excuse me, for this and thank you for your reminder.
May I know your idea about cause of my doubt, Please?
Best Regards
Sara
- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
On 5/10/2012 4:12 PM, mohammad agha wrote:
Dear Mark,
Yes, you're right. Excuse me, for this and thank you for your reminder.
May I know your idea about cause of my doubt, Please?
As I said yesterday:
At least one of your volume, contents or model physics are not
consistent with the
Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, October 5, 2012 9:48 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On
Hello Everybody,
I am using g_covar with -xpmc flag in-oder to generate matrix of
atomic correlation coefficients. At present I am using g_covar script
given by Ran, which I downloaded from gromacs user modified script
pool.
Since Ran's script is for gromacs 3.3.3 and it not accept .trp input
Hi, Justin,
Thank you for your reply.
It is a little weird and inconvienient that genbox does not update the No.
of solute molecules. Is it designed in this way? Does it have any reason
for that?
For my case, the inear, 3-atom model of CO2 works pretty well. I got the
model from a paper from
you have to play with the ratio usually of domain decompositions Vs. Grid size,
I had that error some time ago though, if you look at the generated .mdp from
the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and
play with it. It dosent like odd numbers or non-whole
On 10/5/12 5:18 AM, Bao Kai wrote:
Hi, Justin,
Thank you for your reply.
It is a little weird and inconvienient that genbox does not update the No.
of solute molecules. Is it designed in this way? Does it have any reason
for that?
The principal function of genbox is to solvate systems,
On 10/5/12 5:20 AM, Archana Sonawani wrote:
Dear gromacs users,
I am energy minimizing the TMD (286 residues) in lipid bilayer for
inflategro step. I am getting the following error.
Analysing residue names:
There are: 287Protein residues
There are: 127 Other residues
Analysing
On 10/5/12 5:35 AM, lloyd riggs wrote:
you have to play with the ratio usually of domain decompositions Vs. Grid size,
I had that error some time ago though, if you look at the generated .mdp from
the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and
play with
On 10/5/12 5:49 AM, rama david wrote:
Hi Friends,
I want to study the interaction energy between the selected residues of
protein and ligand.
( Non-bonded energy should include : vanderwall and electrostatics)
How to do it???
This is what the energygrps keyword in the .mdp file is for.
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it
Would you explain me in detail??
With best wishes and regards,
Rama david.
On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 5:49 AM, rama david
On 10/5/12 6:15 AM, rama david wrote:
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it
Would you explain me in detail??
Create a new .tpr file from an .mdp file with suitable energygrps. Use mdrun
-rerun to recalculate
Hi all,
I'm interested in calculating the free-energy change when a frozen part of the
system changes. The change, in general, implies a change in coordinates and in
non-bonded parameters.
As far as I know, there's no efficient way to calculate this currently in
gromacs. The only way I see is
Please unsubscribe. Thank you.
Best,
Marlon
Am 05.10.2012 12:39, schrieb gmx-users-requ...@gromacs.org:
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
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Hi all
I am using g_hbond to calculate the number of hydrogen bonds in an
alcohol system. I am using
the following command:
g_hbond -f traj.trr -nonitacc
I am slightly confused about the cut off r. Using the above command, is
the default cut-off r (0.35nm) for the donor-acceptor distance or the
On 10/5/12 7:20 AM, Gavin Melaugh wrote:
Hi all
I am using g_hbond to calculate the number of hydrogen bonds in an
alcohol system. I am using
the following command:
g_hbond -f traj.trr -nonitacc
I am slightly confused about the cut off r. Using the above command, is
the default cut-off r
On 10/5/12 7:20 AM, Marlon Hinner wrote:
Please unsubscribe. Thank you.
Per the instructions in the footer of every mail on the list:
* Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-requ...@gromacs.org.
-Justin
--
Hi Justin
Thanks, that's what I thought. Is there a need to define a
hydrogen-acceptor distance as well. I read in a few articles that this
was the case, usually 0.25nm ?
Cheers
Gavin
Justin Lemkul wrote:
On 10/5/12 7:20 AM, Gavin Melaugh wrote:
Hi all
I am using g_hbond to calculate the
Hi justin,
thank you for reply.
With best wishes and regards
Rama david.
On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 6:15 AM, rama david wrote:
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
On 10/5/12 7:39 AM, Gavin Melaugh wrote:
Hi Justin
Thanks, that's what I thought. Is there a need to define a
hydrogen-acceptor distance as well. I read in a few articles that this
was the case, usually 0.25nm ?
One can define hydrogen bonds in a number of ways, but a D-A distance of 0.35
Is there any need to use the r2 option the ?
Justin Lemkul wrote:
On 10/5/12 7:39 AM, Gavin Melaugh wrote:
Hi Justin
Thanks, that's what I thought. Is there a need to define a
hydrogen-acceptor distance as well. I read in a few articles that this
was the case, usually 0.25nm ?
One can
On 10/5/12 8:15 AM, Gavin Melaugh wrote:
Is there any need to use the r2 option the ?
That option is not relevant here. It is undocumented in the current release,
but the help description has been updated for the next release:
O.K thanks
Justin Lemkul wrote:
On 10/5/12 8:15 AM, Gavin Melaugh wrote:
Is there any need to use the r2 option the ?
That option is not relevant here. It is undocumented in the current
release, but the help description has been updated for the next release:
Hi all,
I am trying to do a vacuum simulation with distance restrain, first i did an EM
without distance restrastraints, later i did 100 ps to stabilized the T at 300
K but i get this in the pdb file
ATOM 1 N MET 1 nan nan nan 1.00 0.00
ATOM 2 H1 MET 1
On 10/5/12 10:16 AM, rama david wrote:
Hi gromacs friends,
I completed the simulation of receptor and ligand,
I visualized the trajectory in the vmd I found most of the time C terminal
(ARG) interact with receptor ( 320 ASP) .
I want to find out these interaction energy between these two
On 10/5/12 10:16 AM, Paula Andrea Delgado Pinzon wrote:
Hi all,
I am trying to do a vacuum simulation with distance restrain, first i did an EM
without distance restrastraints, later i did 100 ps to stabilized the T at 300
K but i get this in the pdb file
ATOM 1 N MET 1
Thank you Justin For Your Previous reply
Finally Somehow I have Adjusted The Cut-Off and Grid Size and Inserted
Protein in Lipid By Deleting some Lipid Molecules MY Question is
1) When I am
Using inflategro Perl Script ,I
On 10/5/12 10:39 AM, vidhya sankar wrote:
Thank you Justin For Your Previous reply
Finally Somehow I have Adjusted The Cut-Off and Grid Size and Inserted
Protein in Lipid By Deleting some Lipid Molecules MY Question is
1)
Thanks for your reply,
Why could it happen? Can i do something to fix it?
Paula
--
View this message in context:
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Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Dear Gromacs users,
I’m trying to run a REMD simulation on a protein. After a lot of reading,
I am still unclear on the result analysis. Is it correct that, of many
replicas, I should select the frames from only the replica with my desired
temperature?(ex, room temp.) If not correct, how do I
On 2012-10-04 11:50, Emma Eriksson wrote:
Dear all,
I am using the pull code in Gromacs 4.5.5 to constrain the distance in one
direction (z) between a small molecule and a lipid bilayer. I run separate
simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder.
The pull
Thank you for your Help.
I did the following tc-groups
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time constant, in ps
ref_t= 310310 310
On 10/5/12 11:15 AM, pauladelgado wrote:
Thanks for your reply,
Why could it happen? Can i do something to fix it?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
--
Justin A. Lemkul, Ph.D.
On 10/5/12 11:46 AM, rama david wrote:
Thank you for your Help.
I did the following tc-groups
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time
I was able to find reasonable values of kb and b0 and inserted the info into
foplsaabon.itp. I am still getting an error; what I did is the following:
1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check
the section [atomtypes] in fftoplsaa.nb and see to what symbol the
Hi justin,
Ok now I get
I have to modify mdp parameter ..
Thank you,
With best wishes and regards,
Rama david
On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 11:46 AM, rama david wrote:
Thank you for your Help.
I did the following tc-groups
tcoupl
On 10/5/12 1:00 PM, Elie M wrote:
I was able to find reasonable values of kb and b0 and inserted the info into
foplsaabon.itp. I am still getting an error; what I did is the following:
1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check
the section [atomtypes] in
Hi,
I got the result by g_energy.
Thank you for these .
but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put
roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find
Dear all,
I would like to extract the interaction energies (LJ
and electrostatic) between each residue pairs from my trajectory.
The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm,
LJ-SRemat.xpm, totalemat.xpm) but not a data file with
the residue-residue interaction energies I'm
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Bumping this once before the weekend, hoping to get some help.
I am getting segmentation fault errors at 1 to 2 million cycles into my
production MD runs, using GROMACS 4.5.4. If these errors are a consequence
of a poorly-equilibrated system, I am no longer getting the right kind of
error
On 10/5/12 1:26 PM, rama david wrote:
Hi,
I got the result by g_energy.
Thank you for these .
but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put
roup 0WARNING! could not find group (null):extra34-extra34
Thank you a lot,
I only changed the couple-intramol setting (couple-intramol=yes) and now
it´s running just fine. However I have a doubt about something. In the
manual says the following when using couple-intramol=no
In this manner the decoupled state of the molecule corresponds to the
proper
Most often, people only analyze conformations drawn from the target temperature
(e.g. room temperature).
There are reasons to look at higher temperatures (e.g. to decompose
entropy/enthalpy or if your system has
biologically or chemically relevant temperature-dependence) but you can
probably
On 10/5/12 1:40 PM, federico vaglio wrote:
Dear all,
I would like to extract the interaction energies (LJ
and electrostatic) between each residue pairs from my trajectory.
The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm,
LJ-SRemat.xpm, totalemat.xpm) but not a data file
On 10/5/12 3:03 PM, Ladasky wrote:
Bumping this once before the weekend, hoping to get some help.
I am getting segmentation fault errors at 1 to 2 million cycles into my
production MD runs, using GROMACS 4.5.4. If these errors are a consequence
of a poorly-equilibrated system, I am no longer
On 10/5/12 5:19 PM, Sonia Aguilera wrote:
Thank you a lot,
I only changed the couple-intramol setting (couple-intramol=yes) and now
it´s running just fine. However I have a doubt about something. In the
manual says the following when using couple-intramol=no
In this manner the decoupled
Dear Justin , Thank you for your Previous reply
using Genbox I have Successfully Solvated Energy
Minimized System_shrink.gro file It adds 84266 water molecules . Then
Tutorial How to Check Existence of Water Molecules within HydroPhobic core of
Bilayer it is
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