Dear collegues
Thank for advices. Indeed Gromacs is able to analyse two trajectories
with g_rms ( with the flags -f and -f2 ) but as the result I've obtain
graph with one rmsd plot so I'm not sure about implementation of that
method.
So I think that the algorithm proposed by Justin was exactly wh
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 f
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 par
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 is:46S
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 5.3375
Lara Bunte 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 equilibrating and
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 f
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 s
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. So
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 Sand
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 interactio
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
Hi,
Welcome! :-) Sincerely,
Shima
From: marzieh dehghan
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
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Pl
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
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
--
Ju
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 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
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 pl
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?
Sincerel
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 independent
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
ind
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 but
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. Fo
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 R
Thanks Mark ,
I got it now :)
On Thu, Sep 20, 2012 at 3:06 PM, Mark Abraham 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 I have creat
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:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.htm
Thanks!! :) now works!
2012/9/20 Justin Lemkul :
>
>
> 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 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 ACE
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 optio
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 this
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 opinions
thanks a lot Mark
On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham 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 able to find th
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 PDB
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 ca
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 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 desc
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 PDB structure for which I had previous
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 d
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