On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
Dear all,
Why all people cut the protein ligand bond to produce the photodissociation?
Because MM forcefields typically assume bonds do not break or form.
Electronic degrees of freedom are not directly considered in the model.
For instances, In
Thanks Mark.
I was using the following command as I got it in the manual.
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg
But I could not able to find the way how to specify the indices of the
two desired atoms.
( suppose I want to plot the distance between atom no. 500 (protein
Could you tell me what is the procedure to cut the bond to produce
the photodissociation?
On Thu, Sep 20, 2012 at 3:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
Dear all,
Why all people cut the protein ligand bond to produce the
Justin Lemkul wrote
So the initial equilibration was NPT?
Yes.
Justin Lemkul wrote
Did you ever try simply running NVT with
either Berendsen or V-rescale before applying any type of pressure
coupling?
No, I haven't, and I don't remember seeing that described in any work flow.
Justin
On 20/09/2012 4:21 PM, tarak karmakar wrote:
Thanks Mark.
I was using the following command as I got it in the manual.
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg
But I could not able to find the way how to specify the indices of the
two desired atoms.
( suppose I want to plot the
On 20/09/2012 4:34 PM, Ladasky wrote:
Justin Lemkul wrote
So the initial equilibration was NPT?
Yes.
Justin Lemkul wrote
Did you ever try simply running NVT with
either Berendsen or V-rescale before applying any type of pressure
coupling?
No, I haven't, and I don't remember seeing that
Hi Peter,
Thanks for your response.
Rather than dragging this thread too far off-topic, I'll direct you back to
my thread, where I have just posted additional details. I took a warning
message from GROMACS a bit too literally and it caused me to use conditions
that blew up my simulations.
I am
On 2012-09-20 12:18:02AM -0700, Ladasky wrote:
Hi Peter,
Thanks for your response.
Rather than dragging this thread too far off-topic, I'll direct you back to
my thread, where I have just posted additional details. I took a warning
message from GROMACS a bit too literally and it caused
On 20/09/2012 5:08 PM, Ladasky wrote:
Mark Abraham wrote
This all sounds much like an issue with the topology or starting
configuration.
And it is for that reason that, during my debugging process, I switched back
from the chimeric protein structures that I was building myself to a
standard
thanks a lot Mark
On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 20/09/2012 4:21 PM, tarak karmakar wrote:
Thanks Mark.
I was using the following command as I got it in the manual.
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg
But I could not
Dear gmxers,
I have generated MD simulation trajectory using gmx, and now I want to
recalculate the energies and forces for the older trajectory by
excluding interactions between two defined groups. Therefore, the
older trajectory is used as one input option for mdrun through -rerun.
In my
On 20/09/2012 7:31 PM, tarak karmakar wrote:
Dear All,
I need to plot a specific dihedral in my protein and I have to
see how it is changing with time. So while doing that I have created a
new group for that specific dihedral by taking corresponding 4 atoms.
Now, how could I specify
On 20/09/2012 7:26 PM, Wu Chaofu wrote:
Dear gmxers,
I have generated MD simulation trajectory using gmx, and now I want to
recalculate the energies and forces for the older trajectory by
excluding interactions between two defined groups. Therefore, the
older trajectory is used as one input
On 9/20/12 4:24 AM, menica dibenedetto wrote:
Dear all,
I have a problem with pdb2gmx function.
I want to create the gro file of an acetylated at N-term protein.
I copy here the head of the file:
ATOM 2016 HC ACE 0 24.770 -62.381 -11.080 H
ATOM 2015 CT
Thanks!! :) now works!
2012/9/20 Justin Lemkul jalem...@vt.edu:
On 9/20/12 4:24 AM, menica dibenedetto wrote:
Dear all,
I have a problem with pdb2gmx function.
I want to create the gro file of an acetylated at N-term protein.
I copy here the head of the file:
ATOM 2016 HC ACE 0
On 9/20/12 5:18 AM, Ali Alizadeh wrote:
Dear All users
How to create a box of molecules with three layer and a certain number of
molecules?
Use the logical of the biphasic systems tutorial as a basis:
Thanks Mark ,
I got it now :)
On Thu, Sep 20, 2012 at 3:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 20/09/2012 7:31 PM, tarak karmakar wrote:
Dear All,
I need to plot a specific dihedral in my protein and I have to
see how it is changing with time. So while doing that
Dear Gromacs Users!
I'm working with the enssemble of the MD trajectories calculated for
the common protein with the differences in the initial conditions in
the case of each trajectory.
Now I'd like to perform analysis of that enssemble of data. For
example I'de like to obtain RMSD as well as
On 9/20/12 6:06 AM, James Starlight wrote:
Dear Gromacs Users!
I'm working with the enssemble of the MD trajectories calculated for
the common protein with the differences in the initial conditions in
the case of each trajectory.
Now I'd like to perform analysis of that enssemble of data.
Hello!
I am using gromacs for coarse grained systems. I have the need to represent
breakable bonds. I have been using tabulated lennard-jones-cosine
potentials with bonded interactions but now there is a need for proper
non-bonded interactions on specific pairs.
I have went through the manual
Hi,
now I tried it without any restriction and still the LINCS warnings occur.
Since it is always the hydrogen atom where the huge force lies on I had
the idea just to remove the hydrogen atom to find out whether another atom
will occur to have such a high force on or everything went fine. And
On 9/20/12 6:54 AM, Ali Alizadeh wrote:
Dear Justin
I know ,I studied it, but it was two layer, I want to add three layer into
my system!
Right, you're not going to find an exact how-to for everything you might dream
up. You can apply the same logic from the tutorial (creating
Dear Justin
For example, In that tutorial(box vector : 3 , 3 , 10),
At first, I add cyclo hexane into my system( center: 3 ,3 ,1)
Then I add water with certain certain thickness(center: 3 , 3 , 5)
Then I want to add cyclo hexane into my system( center: 3 ,3 , 8)
Is it possible? How to?
Dear Dr.
I might be wrong, but I think you can use g_rms with two seperate trj files,
and it takes the rms from the starting structure of the first one. In which
case you would have to decide which is the reference, and then just do it three
times.
Theres also auxiliarry software which has
On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
now I tried it without any restriction and still the LINCS warnings occur.
Since it is always the hydrogen atom where the huge force lies on I had
the idea just to remove the hydrogen atom to find out whether another
On 9/20/12 7:27 AM, Ali Alizadeh wrote:
Dear Justin
For example, In that tutorial(box vector : 3 , 3 , 10),
At first, I add cyclo hexane into my system( center: 3 ,3 ,1)
Then I add water with certain certain thickness(center: 3 , 3 , 5)
Then I want to add cyclo hexane into my system( center:
On 9/20/12 7:55 AM, cuong nguyen wrote:
Dear Gromacs Users,
Could you please show me the tutorial for liquid-solid simulation?
If it's not at http://www.gromacs.org/Documentation/Tutorials or found by
Google, then it doesn't exist.
-Justin
--
Hi Justin,
thank you a lot for your answer. I will try it.
Best,
Eva
On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
now I tried it without any restriction and still the LINCS warnings
occur.
Since it is always the hydrogen atom where the huge force lies on I
Hi,
Welcome! :-) Sincerely,
Shima
From: marzieh dehghan dehghanmarz...@gmail.com
To: gmx-users@gromacs.org
Sent: Thursday, September 20, 2012 10:11 PM
Subject: [gmx-users] hi
--
gmx-users mailing list gmx-users@gromacs.org
Hello
Could you please take a look on my new pr.mdp file that I created for
equilibrating water around lumiflavin. grompp works but I guess there must be
something wrong because after grompp I am using mdrun and get this warning:
Warning: 1-4 interaction between 1 and 5 at distance 2.429 which
On 9/20/12 3:04 PM, Lara Bunte wrote:
Hello
Could you please take a look on my new pr.mdp file that I created for
equilibrating water around lumiflavin. grompp works but I guess there must be
something wrong because after grompp I am using mdrun and get this warning:
Warning: 1-4
On 20/09/12 01:35, Peter C. Lai wrote:
then switching to nose-hoover for production
runs (as nose-hoover chains result in the correct canonical distribution)?
I was under the impression that v-rescale resulted in the correct
canonical distribution as well. Is this incorrect?
--
Massimo
Hello
In my former questions I got some answers that leads me to following question
(I am really thankful for that. This mailing list and the people here are great
:-) ).
I am using a CHARMM27 force field and it seems that I often used wrong settings
in equilibrating and energy minimization.
On 20/09/2012 9:35 AM, Peter C. Lai wrote:
I am not sure where the idea of using berendsen barostat with the v-rescale
thermostat for equilibration came from, however. Doesn't the typical
equilibration begin with v-rescale for temperature equilibration then
adding parinello-rahman barostat then
I've done some extensive testing (paper on testing method in the
works) and vrescale gives a very accurate ensemble very well for NVT.
Parrinello-Rahman and MTTK are the only algorithms that are correct
for NPT. Berendsen barostat is not. Note that there is a bug with
vrescale + md-vv + that is
Lara Bunte lara.bu...@yahoo.de wrote:
Hello
In my former questions I got some answers that leads me to following
question (I am really thankful for that. This mailing list and the
people here are great :-) ).
I am using a CHARMM27 force field and it seems that I often used wrong
settings in
Dear all,
I am trying to use editconf to produce a .GRO file from an .XYZ file but I am
getting the following error:
Program editconf, VERSION 4.0.5Source code file: futil.c, line: 330
File input/output error:S54NONSOLV.xyz.gro
Some of the input file is:46S54 NONSOLVATED POLYMERC 5.33751
On 9/20/12 8:00 PM, Elie M wrote:
Dear all,
I am trying to use editconf to produce a .GRO file from an .XYZ file but I am
getting the following error:
Program editconf, VERSION 4.0.5Source code file: futil.c, line: 330
File input/output error:S54NONSOLV.xyz.gro
Some of the input file
On 9/20/12 9:35 PM, Rajiv Gandhi wrote:
Dear all gromacs users,
In myoglobin system, how we can cut the bond between Fe-C to produce the
photodissociation through MD?.
I have seen there are number of studies over photodissociation and also
I believe that people have used their appropriate
On 21/09/2012 11:35 AM, Rajiv Gandhi wrote:
Dear all gromacs users,
In myoglobin system, how we can cut the bond between Fe-C to produce the
photodissociation through MD?.
By not making it in your topology. Whatever procedure you follow for
making the other Fe-C interactions needs to differ
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