li lin wants to a share a link on the Gromacs wiki:
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List/Search
li lin says:
Dear all,
Recently I made some tests, and I want to get same potential with the
following method. (gmx 4.0.5.)
Firstly, I run a complete simulation as the
On 24/02/2012 7:05 PM, ros...@kth.se wrote:
li lin wants to a share a link on the Gromacs wiki:
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List/Search
li lin says:
Dear all,
Recently I made some tests, and I want to get same potential with the
following method. (gmx 4.0.5.)
Thank you for your valuble suggestion.
On Fri, Feb 24, 2012 at 12:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 24/02/2012 5:15 PM, Mark Abraham wrote:
On 24/02/2012 4:06 PM, ramesh cheerla wrote:
Dear Gromacs users,
i am planning to use buckingham
My system is a protein-protein complex. After pulling I selected windows
at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and thereafter
windows at 0.2nm spacing was selected upto 7.5nm. In each window 10ns MD
was done and g_wham command was run neglecting the fist 1ns run for
Dear Gromacs Specialists,
I have one problem about g_analyze -ee, May I ask you to help me, Please?
When I do this program as g_analyze -f .xvg -av -ee, it is as followed:
Read 4 sets of 83001 points, dt = 6
std. dev. relative deviation of
Dear Mark,
Thanks for your reply. I am not using both LJ and
Buckingham in the same simulation, but trying to use only Buckingham . As
my system is a polymer which is made of the monomer unit that's what i am
adding to the force field. Our polymer system uses the parameters
Hi GROMACS user,
With the help of command
genbox -ci molecule name -nmol molecule no required
-o out put file -box dimension
I get the desired no of added protein to cell.
But I found that some part of protein is outside
the cell ..
Is such system is good for
shahid nayeem wrote:
My system is a protein-protein complex. After pulling I selected
windows at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and
thereafter windows at 0.2nm spacing was selected upto 7.5nm. In each
window 10ns MD was done and g_wham command was run neglecting the
rama david wrote:
Hi GROMACS user,
With the help of command
genbox -ci molecule name -nmol molecule no required
-o out put file -box dimension
I get the desired no of added protein to cell.
But I found that some part of protein is outside
the cell ..
Is such
I thought this time to be sufficient without any reasonable basis.
shahid Nayeem
On Fri, Feb 24, 2012 at 7:40 PM, Justin A. Lemkul jalem...@vt.edu wrote:
shahid nayeem wrote:
My system is a protein-protein complex. After pulling I selected windows
at 0.1nm from an initial COM distance of
shahid nayeem wrote:
I thought this time to be sufficient without any reasonable basis.
If you pick an arbitrary time frame, you're going to get results with arbitrary
accuracy. Your time frame should be decided based on a whole host of factors,
not the least of which include an
Hi GROMACS community,
I have one problem: I need to calculate the dihedrals for a big system
(so not possible to do it by hand using vmd) starting from a gro file.
Do you know if it exists an efficient way of doing it?
I've seen that the g_chi option exists, however, it doesn't suit for
me as it
francesca vitalini wrote:
Hi GROMACS community,
I have one problem: I need to calculate the dihedrals for a big system
(so not possible to do it by hand using vmd) starting from a gro file.
Do you know if it exists an efficient way of doing it?
I've seen that the g_chi option exists, however,
My protein complex interface has a hydrophobic core and on each side of
this core at the edge are two hydrogen bonds. The Hydrogen bond on one side
is between Arg and Asp and another side it is between Arg and Glu. Its
experimental Kd is in nanomolar regions. How should I decide the length of
the
Dear Gmx Users, Dear Justin
I am wondering which approach for generating velocities in protein or
protein-ligand system is a proper one:
a)
NVT gen_vel = yes
gen_temp=298
gen_seed=-1
NPT gen_vel=no
MDgen_vel=no
b)
NVT gen_vel = yes
gen_temp=298
Thank you both for your replies. I currently have another ionic liquid
running just fine on the same gromacs build (compiled the tpr file
yesterday), so I am reluctant to conclude that the problem is with the
linking. Please let me know if you disagree.
The force field I am using was published
Dear Gromacs users,
Could someone please shed light on the following problem? My system
consists of an alkanethiol SAM (in the xy plane) with a layer of water on
top. The mdrun command works when the box vectors are 1.1, 1.3, and 2.5,
but the SAM flies apart and the simulation crashes. I'm trying
Steven Neumann wrote:
Dear Gmx Users, Dear Justin
I am wondering which approach for generating velocities in protein or
protein-ligand system is a proper one:
a)
NVT gen_vel = yes
gen_temp=298
gen_seed=-1
NPT gen_vel=no
MDgen_vel=no
b)
NVT gen_vel = yes
shahid nayeem wrote:
My protein complex interface has a hydrophobic core and on each side of
this core at the edge are two hydrogen bonds. The Hydrogen bond on one
side is between Arg and Asp and another side it is between Arg and Glu.
Its experimental Kd is in nanomolar regions. How should
Mark,
So as I understood the ussage of X-ray structure as the starting model
where the internal water is already present might be good in case to avoid
those sterric issues doesn't it ?
What are additional options should I use for preparation of such system
with pdb2gmx ? Should I use posres on
Hi, Jochen,
Thanks a lot for your reply. I looked at the example header provided
by g_wham -h. I just wonder if you can answer some more questions for
me.
The example header is
# UMBRELLA 3.0
# Component selection: 0 0 1
# nSkip 1
# Ref. Group 'TestAtom'
# Nr. of pull groups 2
# Group 1
Dear gmx users,
I know this is a old topic. I searched the mailing list however haven't find a
answer.
I am calculating the solvation free energy of a small ligand in water, using
FEP theory. Two steps are applied: firstly decrease the atomic charge to zero;
secondly decrease the VDW to
On 23 February 2012 21:18, Mark Abraham mark.abra...@anu.edu.au wrote:
On 24/02/12, *Juliette N. *joojoojo...@gmail.com wrote:
On 23 February 2012 20:07, Mark Abraham mark.abra...@anu.edu.au wrote:
On 24/02/2012 10:55 AM, Juliette N. wrote:
Hi all,
My average size is 2.9 nm obtained
Dear GROMACS users,
I'm a novice user,
I've been trying to find a way to visualize hydrogen bonds with VMD,but I
haven't been successful.
After running a simulation of 13 Hypericin molecules solved in Water, I loaded
the.gro file and then the trajectory file .xtc, after that in the Create
Hovakim Grabski wrote:
Dear GROMACS users,
I'm a novice user,
I've been trying to find a way to visualize hydrogen bonds with VMD,but
I haven't been successful.
After running a simulation of 13 Hypericin molecules solved in Water, I
loaded the.gro file and then the trajectory file .xtc,
Juliette N. wrote:
On 23 February 2012 21:18, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 24/02/12, *Juliette N. *joojoojo...@gmail.com
mailto:joojoojo...@gmail.com wrote:
On 23 February 2012 20:07, Mark Abraham mark.abra...@anu.edu.au
Try the representation:
all not water
Then set it to the HBONDS
And refer to the VMD mailing list next time! :)
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, February
Dear GROMACS users,
I'm a novice user,
I've been trying to find a way to visualize hydrogen bonds with VMD,but I
haven't been successful.
After running a simulation of 13 Hypericin molecules solved in Water, I loaded
the.gro file and then the trajectory file .xtc, after that in the Create
On 25/02/2012 4:52 AM, Olivia Waring wrote:
Dear Gromacs users,
Could someone please shed light on the following problem? My system
consists of an alkanethiol SAM (in the xy plane) with a layer of water
on top. The mdrun command works when the box vectors are 1.1, 1.3, and
2.5, but the SAM
On 24/02/2012 11:56 PM, ramesh cheerla wrote:
Dear Mark,
Thanks for your reply. I am not using both LJ and
Buckingham in the same simulation, but trying to use only Buckingham .
As my system is a polymer which is made of the monomer unit that's
what i am adding to the
On 25/02/2012 5:37 AM, James Starlight wrote:
Mark,
So as I understood the ussage of X-ray structure as the starting model
where the internal water is already present might be good in case to
avoid those sterric issues doesn't it ?
Yes. This was one of the options I suggested earlier.
Hello,
This email is directed mainly to Alan, who created Acpype.
I've noticed that Acpype has assigned dihedral constants as 0.65084 for many
dihedrals of the form X -c3-n4-X, X -c3-c3-X, and others, in my generated
GROMACS .itp files. These dihedrals have values of 1.400 in the amber
On 24 February 2012 16:52, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
On 23 February 2012 21:18, Mark Abraham mark.abra...@anu.edu.au mailto:
mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote:
On 24/02/12, *Juliette N. *joojoojo...@gmail.com
hello sir,
i was performing simulation for 30ns.
due to queue time limit my mdrun stopped at 11.6ns.. then i extended my
simulation using these two commands
*tpbconv -s md.tpr -extend 2 -o newmd.tpr
mdrun -s newmd.tpr -o md.trr -c md.gro -e md.edr -g md.log -cpi state.cpt
-x traj.xtc
On Sat, Feb 25, 2012 at 12:09 PM, priya thiyagarajan
priya.thiyagaraja...@gmail.com wrote:
hello sir,
i was performing simulation for 30ns.
due to queue time limit my mdrun stopped at 11.6ns.. then i extended my
simulation using these two commands
*tpbconv -s md.tpr -extend 2 -o
Hi
i got that error in the step of pdb2gmx what can i do
i read also
http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database
can any one tell exact reason and how i handle further
thanking you
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