Hi Gianluca,
I have no experience with the -rerun option of mdrun, but my guess is that an
integrated MC/NVT algorithm in GromPy will be faster.
For CGMC, a trial configuration involves generating a new tpr file using
grompp, either with N+1 or N-1 molecules of interest. I implemented such a
Hi
I am trying to use the pull code of gromacs (version 4.5.5) to constrain the
com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group
(labelled GOLD). This is the segment of the .mdp file I have used:
;CoM pull calculations
pull= constraint
Dear Gromacs Users,
i have data for the distance between the protein and water atoms within a
cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze
on this data. The time frame in the output data is not continuous because
of the cut off provided. So i would like to know how
Hi everyone!
I tried doing H-bond analysis using g_hbond on a solute dissolved in water. The
solute has hydroxyl groups. In an attempt to analyze water-bridges formed thru
H-bonds, I noticed that g_hbond does not seem to give consistent results. As
previously discussed in this list, I am
You should first make an *.itp file for DPPC, then include it in the *.top
file. whatever that is not in GROMACS library should be defined to it. You
would better see http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf , hope it
will help.
From: Anushree
Anushree Tripathi wrote:
But in coordinate file(.pdb file) ,I am not getting the atoms which
belongs to DPPC.only I have included the name of dppc.itp file like this:
This is precisely the problem - you have no DPPC in the coordinate file.
;Include DPPC chain topology
#include dppc.itp
On 1/02/2012 6:25 PM, Anushree Tripathi wrote:
But in coordinate file(.pdb file) ,I am not getting the atoms which
belongs to DPPC.
You cannot do anything unless you have a coordinate file that includes
DPPC coordinates. I don't know how to express this any more clearly.
only I have
dina dusti wrote:
Dear Prof.
Thank you very much from your response.
Yes, dist.xvg has four column consists origin distance and distances in
direction x, y , z. So distance that I want according to result of
g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups,
micelle and
Dear all;
Through the MD simulation for a DNA, I wonder whether we should change
any options for the terminal bases or not.
Thank you in advance
B.Mehrazma
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Wright, Louise wrote:
Hi
I am trying to use the pull code of gromacs (version 4.5.5) to constrain
the com of a number of groups (labelled CIT, CIT1, CIT2...) to a
reference group (labelled GOLD). This is the segment of the .mdp file I
have used:
;CoM pull calculations
pull
aiswarya pawar wrote:
Dear Gromacs Users,
i have data for the distance between the protein and water atoms within
a cut off of 8A for 5ns using the g_dist option. Now i want to use
g_analyze on this data. The time frame in the output data is not
continuous because of the cut off provided.
Banafsheh Mehrazma wrote:
Dear all;
Through the MD simulation for a DNA, I wonder whether we should change
any options for the terminal bases or not.
What is it that you think you should change?
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000.62590240.3880.3610001 -0.3329997
1.0000.67787750.25900030.593 -0.198
2.0000.67590300.25299980.593 -0.203
On 2/02/2012 12:28 AM, aiswarya pawar wrote:
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000.62590240.3880.3610001 -0.3329997
1.0000.67787750.25900030.593 -0.198
2.000
aiswarya pawar wrote:
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000.62590240.3880.3610001 -0.3329997
1.0000.67787750.25900030.593 -0.198
2.0000.67590300.2529998
Hi Justin,
thanks for your reply. Yes the distances get a lot larger and are definitely
not just fluctuating. It is hard to demonstrate this without showing you the
whole file which is huge. However, I have used the same input files with
gromacs 4.5.4 just now and it works- I think it might
Wright, Louise wrote:
Hi Justin,
thanks for your reply. Yes the distances get a lot larger and are
definitely not just fluctuating. It is hard to demonstrate this without
showing you the whole file which is huge. However, I have used the same
input files with gromacs 4.5.4 just now and
If i give command as =
g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8
this prints out all the protein water distance within 0.8nm. The data printed
out is such that=
t: 1466 5369 SOL 20624 OW 0.789894 (nm)
t: 1467 5369 SOL 20624 OW 0.781596 (nm)
t: 1469 5369 SOL 20624 OW 0.785377 (nm)
aiswarya pawar wrote:
If i give command as =
g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8
this prints out all the protein water distance within 0.8nm. The data printed
out is such that=
t: 1466 5369 SOL 20624 OW 0.789894 (nm)
t: 1467 5369 SOL 20624 OW 0.781596 (nm)
t: 1469 5369
So,
This is slightly aside from the installation of the openMM (cuda), but is CUDA
related.
Does anyone know the state of the CUDA to OpenCL porting the AMD (CUDA teams
said they were going to do this) and then further all CUDA work as OpenCL, as
no one has mentioned anything on this since
hi all...
ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı
use below mdp file
; Run control
integrator = sd ; Langevin dynamics
tinit= 0
dt = 0.002
nsteps = 5; 100 ps
nstcomm
Hi all,
The NAIS Centre in Edinburgh is holding a Workshop on State-of-the-Art
Algorithms for Molecular Dynamics on May 2-4.
The days before this workshop, April 30-May 2, I and David Hardy from NAMD will
organize a tutorial on the use of GPUs and parallel computing. Here, among
other things,
Dear Prof.
Thank you very much from your response.
but I didn't select micelle headgroups and then terminal carbon atom but also I
selected COM of micelle and for example head group of micelle! The calulation
of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but
g_dist
Dear Prof.
Thank you very much from your reply.
Is your mean that density=(N/V)*g(r), where N is the number of total atoms in
box not in the shell and V is the volume of box not in the shell?
Best Regards
Sara
From: Dallas Warren dallas.war...@monash.edu
Dear Prof.
Thank you very much from your response.
I removed pbc and jump in my system, and when I see my system as visual in
ngmx, there is not pbc and jump and has been created one micelle and it remain
stable for long times.
I really don't know what should I do!
Best Regards
Dina
--
Dear Gromacs users,
I want to use the Gromacs analysis tools for analyzing Namd output files
(*.dcd files) I just installed Gromacs 4.5.4 and it works well. In addition
I installed VMD 1.9 and set up
VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is
located the dcdplugin.so
mehmet kıytak wrote:
hi all...
ı have a problem.. ı got segmentation fault when run nvt equilibration..
ı use below mdp file
Please post a complete .mdp file. The Unix 'cat' command can be used to print
the contents of the text file, which can then be copied and pasted into an email.
dina dusti wrote:
Dear Prof.
Thank you very much from your response.
but I didn't select micelle headgroups and then terminal carbon atom but
also I selected COM of micelle and for example head group of micelle!
The calulation of radius of micelle by radius of gyration give that is
near
Dear Prof.
Thank you very much for your help.
Yes, I also used from g_rdf and g_gyrate but I am seeking root-mean-square
distance that there is in many articles for calculation of radius of micelle
and radius of dry core (hydrocarbone). I understood that they used g_dist but
it doesn't work
dina dusti wrote:
Dear Prof.
Thank you very much for your help.
Yes, I also used from g_rdf and g_gyrate but I am seeking
root-mean-square distance that there is in many articles for
calculation of radius of micelle and radius of dry core (hydrocarbone).
I understood that they used g_dist
Dear Prof.
Thank you very much from your response.
He answer me that I should use from g_gyration for radius of micelle, but what
should I do for hydrocarbon (dry) core or calculation of inner core of micelle
(i.e. the first of carbon on tail of surfactant with COM of micelle)?
Best Regards
hi justin
ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron
distance edge 2.0 nm.
; Run control
integrator = sd ; Langevin dynamics
tinit= 0
dt = 0.002
nsteps = 250 ; 5 ns
nstcomm
mehmet kıytak wrote:
hi justin
ı used this mdp. file ..simulation box may be wrong.?..ı used
dodecahedron distance edge 2.0 nm.
No, that's almost certainly not the problem. Insufficient
minimization/equilibration, or instability due to the use of the free energy
code is more
dina dusti wrote:
Dear Prof.
Thank you very much from your response.
He answer me that I should use from g_gyration for radius of micelle,
but what should I do for hydrocarbon (dry) core or calculation of inner
core of micelle (i.e. the first of carbon on tail of surfactant with COM
of
On 2/02/2012 2:08 AM, aiswarya pawar wrote:
If i give command as =
g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8
this prints out all the protein water distance within 0.8nm. The data printed
out is such that=
t: 1466 5369 SOL 20624 OW 0.789894 (nm)
t: 1467 5369 SOL 20624 OW 0.781596
On 2/02/2012 4:35 AM, PAUL NEWMAN wrote:
Dear Gromacs users,
I want to use the Gromacs analysis tools for analyzing Namd output
files (*.dcd files) I just installed Gromacs 4.5.4 and it works well.
In addition I installed VMD 1.9 and set up
d(r) = (N/V)*g(r)
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer,
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
for a few interactions, with each of them approaching inf.
On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling selin...@msu.edu wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase
On 2/02/2012 3:36 PM, Alex Seling wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
for a few
On 2/02/2012 3:42 PM, lina wrote:
On Thu, Feb 2, 2012 at 12:36 PM, Alex Selingselin...@msu.edu wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp
Please suggest me the exact way to include dppc coordinates in topol.top
file.
On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 1/02/2012 6:25 PM, Anushree Tripathi wrote:
But in coordinate file(.pdb file) ,I am not getting the atoms which
belongs to DPPC.
Are you actually trying to simulate a membrane protein inside a DPPC bilayer
though? If not, what is your reason for having it in your system?
Also the topol.top file does not contain coordinates at all, only the
forcefield parameterization.
On 2012-02-02 12:11:44PM +0530, Anushree Tripathi
On 2/02/2012 5:41 PM, Anushree Tripathi wrote:
Please suggest me the exact way to include dppc coordinates in
topol.top file.
Start here
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations, as I
think Justin already suggested. You should definitely learn (about)
other people's
Yes I want to simulate the protein inside DPPC bilayer but how could I make
the index file. Everytime it is showing error that no DPPC found in index
file.
On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai p...@uab.edu wrote:
Are you actually trying to simulate a membrane protein inside a DPPC
Hi,
I'm studying the diffusion system of some guest into zeolite structure
(SiO2) assumed to be rigid body.
My question is about making the host neutral.
I obtained the unit cell of zeolite structure from the web.
The structure exhibit net charge. (If I give some charge to Si and O which
Ok. You will:
1. Need an actual DPPC bilayer. You can either make one from scratch (using
something like VMD), or use pre-equilibrated patches from other people (like
the ones from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
(dppc128.pdb from that site).
2a. The
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