> Message: 2
> Date: Thu, 26 Jul 2012 20:56:00 +1000
> From: Mark Abraham
> Subject: Re: [gmx-users] Writing velocity of particles using
> template.c
> To: Discussion list for GROMACS users
> Message-ID: <50112240.5000...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=
Hi everybody,
I want to minimize only the hydrogen atoms of my protein but NOT the rest
of it. For this reason I use a restriction file produced by pdb2gmx with
the -i option.
But still the atoms are minimized a bit. Because when I calculate the RMSD
with the program g_confrms of my structure befor
On Fri, Jul 27, 2012 at 11:37 AM,
wrote:
> Hi everybody,
> I want to minimize only the hydrogen atoms of my protein but NOT the rest
> of it. [...]
> SO is there are possibility to completely fix those atoms. So that they
> just do not move?
>
You can try the freezegrps and freezedim options in t
Thank you!!
> On Fri, Jul 27, 2012 at 11:37 AM,
> wrote:
>> Hi everybody,
>> I want to minimize only the hydrogen atoms of my protein but NOT the
>> rest
>> of it. [...]
>> SO is there are possibility to completely fix those atoms. So that they
>> just do not move?
>>
>
> You can try the freezegr
Hi,
Is GROMACS package has any advantages over NAMD?
Your suggestions would be appreciated.
Sincerely,
Shima
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Hi,
Does GROMACS package have any advantages over NAMD?
Your suggestions would be appreciated.
Sincerely,
Shima
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Hi Justin, Thanks for that information.
I also would like to confirm with you that should I combine my metal ion too
while I combine Protein and POPC into Protein_POPC group to be used in COMM
removal? So that I will have a group Protein_HEM_POPC.
Thanks
Peterson J
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On 27/07/2012 9:05 PM, Shima Arasteh wrote:
Hi,
Does GROMACS package have any advantages over NAMD?
Yes, but the real question is which package provides the best scientific
return for your time and your computer time, given your simulation
problem, your hardware and your experience with ea
On 27/07/2012 7:14 PM, prithvi raj pandey wrote:
Message: 2
Date: Thu, 26 Jul 2012 20:56:00 +1000
From: Mark Abraham
Subject: Re: [gmx-users] Writing velocity of particles using
template.c
To: Discussion list for GROMACS users
Message-ID: <50112240.5000...@anu.edu.au>
Content-Type: tex
Dear All,
I just configured the mdrun-gpu. When I tested "mdrun-gpu" by running
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it
failed with segmentation fault. I don't think the system has any equilibrium
problem since it works fine in "mdrun". I will appreciate a
Thanks dear Mark for your reply.
It was just a simple question, liked to hear answers from the one who knows
more about the simulation packages more than me. Again thanks dear Mark.
In my own, I've only worked with GROMACS and don't have any experiences of
NAMD.
About the problem which I want
On 7/27/12 10:58 AM, Shima Arasteh wrote:
Thanks dear Mark for your reply.
It was just a simple question, liked to hear answers from the one who knows
more about the simulation packages more than me. Again thanks dear Mark.
In my own, I've only worked with GROMACS and don't have any experienc
On 7/27/12 8:50 AM, J Peterson wrote:
Hi Justin, Thanks for that information.
I also would like to confirm with you that should I combine my metal ion too
while I combine Protein and POPC into Protein_POPC group to be used in COMM
removal? So that I will have a group Protein_HEM_POPC.
With
Hi,
Thanks, Justin! Is it possible to set the start time as t = 10 ns instead
of t = 0? When I pass the checkpoint to grompp with -t, the simulation
starts at t =0 by default. Is there a way to change this, such that I will
be able to easily concatinate the two trajectories using trjcat (i.e.,
On 7/27/12 11:31 AM, Andrew DeYoung wrote:
Hi,
Thanks, Justin! Is it possible to set the start time as t = 10 ns instead
of t = 0? When I pass the checkpoint to grompp with -t, the simulation
starts at t =0 by default. Is there a way to change this, such that I will
be able to easily concat
Mark,
You are right. I've run gmxdump on the eigenvectors and I can see nan
coordinates in 3 consecutive frames (13589 to 13591):
eigenvectors.trr frame 13589:
natoms= 4600 step= 13588 time=-3.2829557e-06 lambda= 0
box (3x3):
box[0]={ 0.0e+00, 0.0e+00,
hi everybody
i want to calculate the P_N orientation of dppc lipid bilayer but in g_angle
index file shoud have at least 3 atom but in P_N vector i want to define 2 atom
is there anyone know what should i do?
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On 7/27/12 12:50 PM, yousef nademi wrote:
hi everybody
i want to calculate the P_N orientation of dppc lipid bilayer but in g_angle
index file shoud have at least 3 atom but in P_N vector i want to define 2 atom
is there anyone know what should i do?
g_sgangle with the -z option (assuming
- Forwarded Message -
From: yousef nademi
To: Justin Lemkul
Cc:
Sent: Friday, July 27, 2012 10:02 AM
Subject: Re: [gmx-users] p_N head group lipid orientation
thank you for responding
but i want the figure probability versus P-N vector angle and g_sgangle dont
give this output .ju
Which parameter is supposed to be changed to get the sufficient minimized
system? Would anyone guide me please?
Thanks in advance
Cheers,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Wednesday, July 25, 2012 4:37 PM
Subject: Re: [
Hi all -
Is there any plan to get LINCS working with the MTTK barostat in the near
future?
Thanks
Katie
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On 7/27/12 1:02 PM, yousef nademi wrote:
thank you for responding
but i want the figure probability versus P-N vector angle and g_sgangle dont
give this output .just g_angle give this output
g_analyze -distr produces distributions from any .xvg file, otherwise it is
fairly straightforward
On 7/27/12 1:08 PM, Shima Arasteh wrote:
Which parameter is supposed to be changed to get the sufficient minimized
system? Would anyone guide me please?
This question is very vague. In principle, any system can be minimized but the
definition of "sufficient" depends on your goals.
-J
As I explained here before, I get an error ( some interactions seem to be
assigned multiple times). I suspected the top file, so checked it and
visualized the output of em.mdp; the output seems to be correct and I don't see
any bonds behaves strangely.
As I studied in mailing lists it and yo
HI everybody,
I want to do a minimization and a md run with my protein. But I only want
the hydrogen atoms to be minimized but not the rest of the protein.
I use the
freezegrps = Protein-H
freezedim = Y Y Y
option in my mdp files to make sure that they don't change.
During the minimization steps
Among simulation people at my institution, all the other lipids people
use NAMD. This was mostly a user-experience decision. When they started
their work, NAMD had better parallelization (this was before Gromacs 4+
came out). Now even though Gromacs has great parallelization, they don't
see a reas
:)
Thanks dear Peter.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Discussion list for GROMACS users
Cc:
Sent: Saturday, July 28, 2012 2:16 AM
Subject: Re: [gmx-users] GROMACS OR NAMD
Among simulation people at my institution, all the other lipids people
use NAM
Dear Justin,
Thanks for your quick reply. Actually, we think that the topology is OK,
however HAP's parameters could be wrong, we are checking on this...
These are the topology files used for HAP. The names associated to the atoms
present on the slab are:
ACa - Ca2+
AP - P
AO1 - O(P)
AO4 - O(
On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote:
Dear All,
I just configured the mdrun-gpu. When I tested "mdrun-gpu" by running
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it failed with
segmentation fault. I don't think the system has any equilibrium proble
>
> I want to do a minimization and a md run with my protein. But I only want
> the hydrogen atoms to be minimized but not the rest of the protein.
> I use the
> freezegrps = Protein-H
> freezedim = Y Y Y
>
> option in my mdp files to make sure that they don't change.
>
> During the minimization st
On 28/07/2012 4:34 AM, Shima Arasteh wrote:
As I explained here before, I get an error ( some interactions seem to be
assigned multiple times).
And it's been suggested several times that your system may be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, and
diagnostic and manag
Hello Mark,
Thanks for your reply. It has taken me several days to make some progress
on my issues. I'm just going to address one specific point in this post.
Mark Abraham wrote
>
> On 19/07/2012 6:52 PM, Ladasky wrote:
>
>> I once used the -deuterate option in pdb2gmx, and I am presently tr
On 7/27/12 9:55 PM, Ladasky wrote:
Hello Mark,
Thanks for your reply. It has taken me several days to make some progress
on my issues. I'm just going to address one specific point in this post.
Mark Abraham wrote
On 19/07/2012 6:52 PM, Ladasky wrote:
I once used the -deuterate option i
On 7/27/12 8:54 PM, Ramon Garduno wrote:
Dear Justin,
Thanks for your quick reply. Actually, we think that the topology is OK,
however HAP's parameters could be wrong, we are checking on this...
I would say that the topology being OK and the parameters being wrong are
contradictory stateme
Good question. Short answer, no -- LINCS doesn't play well with a
velocity verlet based pressure control algorithm.
Long answer: MTTK has ended up not being robust because you need to
solve a self consistent set of equations every timestep using the
pressure estimator, which is extremely noisy, s
Hi,
my problem is, that during the md run the atoms are not frozen somehow.
During the minimization run everything worked out fine. But when I did a
md run the hydrogen atoms and the other atoms seems to be changes somehow.
I calculated the RMSD value and this is why I know that they change.
After
Hi,
I am intending to calculate binding affinity using Linear Interaction
method (LIE method) for which I need to perform two simulations for
given ligand both in free and bound states and get the values of
Electrostatic and Van der Waals Interaction energies of the ligand.
I have done simulation
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