On 11/06/2012 12:41 AM, Justin A. Lemkul wrote:
On 6/10/12 10:36 AM, Andrew DeYoung wrote:
Greetings,
This might end up being a silly/embarrassing question, and if so, I
apologize. I feel like I may be making a conceptual mistake, but I'm
not
sure.
Is it true that a hydrogen bond is of
Hi Gromacs Friends ..
I am trying to simulate octa-peptide in water model spc using G96 53a6
force field.
my aim is to study the self assembly nature of these octapetide.
I did following type of arrangment.
I make antiparrallel arrangment of four peptide with distance of 0.5 nm in
y direction,
On 10/06/2012 5:50 PM, Inon Sharony wrote:
Hi Mark! Thanks for the response. Just to follow up, the problem was
that another program was deleting md.log before it could be accessed.
This is entirely not the fault of GROMACS, however a more descriptive
error message could have saved us some
On 11/06/2012 4:38 PM, rama david wrote:
Hi Gromacs Friends ..
I am trying to simulate octa-peptide in water model spc using G96 53a6
force field.
my aim is to study the self assembly nature of these octapetide.
I did following type of arrangment.
I make antiparrallel arrangment of four
On 11/06/2012 4:58 PM, Seera Suryanarayana wrote:
Dear all gromacs users,
i am running md using gromacs
software.I want to down load minim.mdp file for creating a em.tpr
file.But i don't know where i can get this file and how to download
this file.
There is
Hi MARK,
Thank you to your Quick reply,
Please accept my apology for incomplete information...
I did simulationm of single, Double and four peptide..
I also tried following
I make antiparrallel arrangment of four peptide with distance of 0.4 nm in
y direction,
Then I translate these layer in
Hello again fellow gromacs users.
I am looking to model a glucose-rhamnose disaccharide using the 53a6
forcefield. I wanted to take a look at the naming conventions for
carbohydrates but I'm battling to find anything in the pdb2gmx force field
files.
I downloaded a package of force fields from
On 11/06/2012 5:49 PM, rama david wrote:
Hi MARK,
Thank you to your Quick reply,
Please accept my apology for incomplete information...
I did simulationm of single, Double and four peptide..
I also tried following
I make antiparrallel arrangment of four peptide with distance of 0.4
nm in y
Justin
1) So if I understood correctly I can make parametrisation of my uncommon
group by the atb for instance. Than I can change itp file to rtp form and
integrate this new residue to the existing ff. Finally when I will run
pdb2gmx on the protein with the same group (even with different atom
On 11/06/2012 6:11 PM, Marc Gordon wrote:
Hello again fellow gromacs users.
I am looking to model a glucose-rhamnose disaccharide using the 53a6
forcefield. I wanted to take a look at the naming conventions for
carbohydrates but I'm battling to find anything in the pdb2gmx force
field files.
Dear all gromacs users,
While i am running the commond mdrun -v
-deffnm em iam getting the following error.
Fatal error:
Domain decomposition does not
support simple neighbor searching, use grid
On 11/06/2012 6:12 PM, James Starlight wrote:
Justin
1) So if I understood correctly I can make parametrisation of my
uncommon group by the atb for instance. Than I can change itp file to
rtp form and integrate this new residue to the existing ff. Finally
when I will run pdb2gmx on the
On 11/06/2012 6:21 PM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am running the commond mdrun
-v -deffnm em iam getting the following error.
Fatal error:
Domain decomposition does
Dear Justin sir,
I am simulating a protein 1AKI.pdb which is example of
your tutorial.I am doing simulations as your tutorial.I didnt get any
errors upto the commond grompp -f minim.mdp -c 1AKI_solv_ions.gro -p
topol.top -o em.tpr.After this as your tutorial i used the commond
Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to
calculate it via MD simulation for calcium pump protein. Following the
same method as described in justin lezozyme tutorial, we have dissolved
the protein in water.
I want to know that is it wise to study this
Dear all!
Recently I've forced with the opposite problem. I have pre-equilbrated
bilayer of highter dimensions than I need. How I could reduce lipid number
of such bilayer as well as reduce total dimensions of such system ?
E.g I have preequilibrated bilayer consisted of 340 lipids. I want to
Have you tryed online servers as
http://davapc1.bioch.dundee.ac.uk/prodrg/or the Acpype (with Amber)?
2012/6/11 Marc Gordon marcgrd...@gmail.com
Hello again fellow gromacs users.
I am looking to model a glucose-rhamnose disaccharide using the 53a6
forcefield. I wanted to take a look at the
On 6/11/12 6:05 AM, James Starlight wrote:
Dear all!
Recently I've forced with the opposite problem. I have pre-equilbrated bilayer
of highter dimensions than I need. How I could reduce lipid number of such
bilayer as well as reduce total dimensions of such system ?
E.g I have
On 6/11/12 5:20 AM, delara aghaie wrote:
Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to calculate it
via MD simulation for calcium pump protein. Following the same method as
described in justin lezozyme tutorial, we have dissolved the protein in water.
I
On 6/11/12 6:06 AM, Thales Kronenberger wrote:
Have you tryed online servers as http://davapc1.bioch.dundee.ac.uk/prodrg/ or
the Acpype (with Amber)?
For Gromos parameterization, ATB produces much better results than PRODRG.
http://compbio.biosci.uq.edu.au/atb/
Validation is always
Dear All,
Sorry to trouble you with the same question, but my question from last
friday was probably badly formulated, so I'll try again.
Assume our system consists of ten atoms (atom indexes 1-10).
It has two groups,
group A has atoms 1, 7, 9
group B has atoms 2-6, 8, 10
Is it possible (either
Hi Mark,
I did simulation of the same system in vacuum, and system behave the
normally,
So the instability in the system is due to the spc Water model???
As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up
I think the source is (Please tell me is it right..?? or any else
On 6/11/12 6:23 AM, rama david wrote:
Hi Mark,
I did simulation of the same system in vacuum, and system behave the normally,
So the instability in the system is due to the spc Water model???
As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up
The water model is
Hi Justin, thank you for quick reply.
You are right I have practicle result, And I want to replicate them..
Thank you for your suggestion..
With Best Wishes,
Rama David
On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 6/11/12 6:23 AM, rama david wrote:
Hi
Hi gmx users,
I'm trying to create an equilibrated 2,3 dihydroxynaphthalene solvent box. I
used PRODRG2 server to create an itp file from the
downloaded pdb file. I used genbox to insert the solvent randomly into a 5
nm cubic box. Then I energy minimised it and did NVT and NPT equilibration
on
On 6/11/12 6:42 AM, Satish Kamath wrote:
Hi gmx users,
I'm trying to create an equilibrated 2,3 dihydroxynaphthalene solvent box. I
used PRODRG2 server to create an itp file from the
downloaded pdb file. I used genbox to insert the solvent randomly into a 5
nm cubic box. Then I energy
Dear Justin.
Thanks for your explanation.
In lyzozyme tutorial the radius of gyration has been plooted against simulation
time (there 1000 ps).
When I plot the same graph, the horizontal axis is up to 500 (The number of
frames for data
On 6/11/12 8:40 AM, delara aghaie wrote:
Dear Justin.
Thanks for your explanation.
In lyzozyme tutorial the radius of gyration has been plooted against simulation
time (there 1000 ps).
When I plot the same graph, the horizontal axis
Dear Justin
My question can be related to both. Ok let me talk about the tutorial. The
simulation has finished compeletly and log file and other outputs show the
completion of 1 ns simulation.
this is part of gyrate.xvg file I see:
-
@ s0 legend Rg
@ s1 legend RgX
@ s2 legend RgY
@
On 6/11/12 9:09 AM, delara aghaie wrote:
Dear Justin
My question can be related to both. Ok let me talk about the tutorial. The
simulation has finished compeletly and log file and other outputs show the
completion of 1 ns simulation.
this is part of gyrate.xvg file I see:
-
@ s0
Dear Justin
Thanks again. Ok I got it.
Only there remains a question:
you mean it is possible that the simulation has finished for 1 ns but the .xtc
file does not have the information for whole frames or even it is possible for
g_gyrate program to crash and give the non-compelete .xvg file?
On 6/11/12 9:28 AM, delara aghaie wrote:
Dear Justin
Thanks again. Ok I got it.
Only there remains a question:
you mean it is possible that the simulation has finished for 1 ns but the .xtc
file does not have the information for whole frames or even it is possible for
g_gyrate program to crash
hi
sorry 4 not doing it before, right now am doing Solvate the Box step in
molecular modelling am using Gromacs 4.5.5 ver
during the first step i.e creating the topology file ,i tried to create
the topology file by using the command
pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.pdb –p fws.top
On 6/11/12 9:54 AM, ramaraju801 wrote:
hi
sorry 4 not doing it before, right now am doing Solvate the Box step in
molecular modelling am using Gromacs 4.5.5 ver
during the first step i.e creating the topology file ,i tried to create
the topology file by using the command
pdb2gmx –ignh –ff
Dear Sir,
Thank you for your response. I've read the paper and will look into the
charge distribution.
Thank you once again.
Satish Kamath
IISc Bangalore
India
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Justin and Mark,
Thank you SO much for your help!
Andrew DeYoung
Carnegie Mellon University
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Thank you very much for your answer,
After setting up some qm/mm runs, I clearly understand what you mean.
Wow, the qm calculations are some cpu eating monsters...
M.
On Fri, Jun 8, 2012 at 3:46 PM, Gerrit Groenhof ggro...@gwdg.de wrote:
YOucan only use one thread in mdrun, but more than one in
Hi,
I am analyzing hydrogen bonds using g_hbond. I have selected two
non-overlapping groups; one is hydroxyl groups (OH, where O is the donor and
H is the hydrogen), and the other is oxygens on PO4^3- (where F is the
acceptor). I am using the switch -noda, which tells the program to take the
Hi again,
I just realized that the output from g_hbond using the -num flag (by
default, the file name is hbnum.xvg) also seems to make a distinction
between hydrogen bonds and pairs within the distance. For example, here
are the first few lines of this output file:
@ s0 legend Hydrogen bonds
@
On 6/11/12 5:41 PM, Andrew DeYoung wrote:
Hi again,
I just realized that the output from g_hbond using the -num flag (by
default, the file name is hbnum.xvg) also seems to make a distinction
between hydrogen bonds and pairs within the distance. For example, here
are the first few lines of
On 11/06/2012 8:22 PM, Markus Kaukonen wrote:
Dear All,
Sorry to trouble you with the same question, but my question from last
friday was probably badly formulated, so I'll try again.
Assume our system consists of ten atoms (atom indexes 1-10).
It has two groups,
group A has atoms 1, 7, 9
group
Dear All ,
I am facing problem in matching the coordinates number in this two files,
em.gro and toplogy.top.
I have tried with changing the number of solvents, adding ions (Na+)
but in vain
*Note :: My system has ' -1.00 ' charge ...so I have added one Sodium
ion*
So can anyone please
Could you paste your .top file and the command your add ions? Maybe the Cl-
ion was also added when you added Na+ ion?
On Tue, Jun 12, 2012 at 1:18 PM, tarak karmakar tarak20...@gmail.comwrote:
Dear All ,
I am facing problem in matching the coordinates number in this two files,
em.gro and
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