Hi!
Is it possible to specify which residues to restrain during MD simulation?
For example I have a protein, but I don't want to restrain all the
molecule, but a part.
How can I do this?
--
Андрей Гончар
--
gmx-users mailing listgmx-users@gromacs.org
On 31/01/2012 7:06 PM, Андрей Гончар wrote:
Hi!
Is it possible to specify which residues to restrain during MD simulation?
For example I have a protein, but I don't want to restrain all the
molecule, but a part.
How can I do this?
See
So for every residue I need to specify their atoms, am I right?
2012/1/31 Mark Abraham mark.abra...@anu.edu.au:
On 31/01/2012 7:06 PM, Андрей Гончар wrote:
Hi!
Is it possible to specify which residues to restrain during MD simulation?
For example I have a protein, but I don't want to
On 31/01/2012 7:14 PM, Андрей Гончар wrote:
So for every residue I need to specify their atoms, am I right?
Yeah. One way is to use make_ndx to select the atoms in the residues and
make an index file group, then genrestr, then #include the generated
.itp file.
Mark
2012/1/31 Mark
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know that I should use g_rdf. Then I count the number of
atoms in the shells around the COM of special group by trjorder -com -nshell
-r , next I use from this formula for compute
Hi Gianluca,
Ah, I get it. In that case you can actually use GromPy, but it needs to be
modified slightly. You need only one tpr file that will be stored in memory
during execution of GromPy. For the sampling you can generate new
configurations and accept/reject them according to the
Hello,
Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job. please
help.
The following is a part of the dna pdb file, which I am using:
ATOM 1 O5' DG5 X 1 13.663 36.760 21.465 0.00 0.00
ATOM 2 C1' DG5 X 1
- Forwarded Message -
From: mohammad agha mra...@yahoo.com
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Tuesday, January 31, 2012 11:56 AM
Subject: g_rdf
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know
Dear GMX users,
We want to develop the ff parameters for some small molecules in consistent
with gromos 53a6, and I know that PRODRG can do it, but it is not accurate
enough. So we want to do some QM calculations to validate it. However, how
can I derive these parameters for bonds and dihedrals
On 2012-01-31 11:28, Qinghua Liao wrote:
Dear GMX users,
We want to develop the ff parameters for some small molecules in
consistent with gromos 53a6, and I know that PRODRG can do it, but it is
not accurate enough. So we want to do some QM calculations to validate
it. However, how can I derive
Dear gmx users
I have done umbrella sampling for a membrnae drug system and i have
used 13 windows in this process but at last when I extracted the
histogram curve I only had two peak.Is this reasonable?
Also my PMF curve has several minimum and maximum points and at last
it converges to zero.Is
Anushree Tripathi wrote:
I am using gromacs 4.5.3 version.When I run the command (i.e., make_ndx
-f em.gro -o index.ndx),It is not showing any option for DPPC group
which I want to include.Please tell me how could I merge or create this
option for proceeding to the next step of NVT
francesca vitalini wrote:
Hallo GROMACS users!
I'm trying to run a simple md script after running an energy
minimization script on my system and I'm getting a wired error message
Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precision)
Loaded with Money
Maryam Hamzehee wrote:
Hi
Many thanks for your email, the question is that topology file (*.top)
has not DNA, if I want to produce the tpr file I need a top file
containing both DNA and protein; How can I edit my top file in oredr to
include DNA in my top file.
Then you need to
Hi,
I'm compiling gromacs 4.5.5 with gcc compiler (v 4.5.3), cmake (2.8.7) and
OpenMM 3.1.1 on Linux (Red Hat release 5.7). I have followed the installation
instructions.
The configuration seems to work well.
~/progs/cmake-2.8.7/bin/cmake -DGMX_OPENMM=ON
parto haghighi wrote:
Dear gmx users
I have done umbrella sampling for a membrnae drug system and i have
used 13 windows in this process but at last when I extracted the
histogram curve I only had two peak.Is this reasonable?
No. If you conducted 13 simulations, you should have 13
Actually the directory is of my own and I have created it in my home directory
so that shouldn't be a problem as I also have created other files in the same
directory without any problems so far.
Other ideas?
Thanks
Francesca
Il giorno 31/gen/2012, alle ore 13.02, Justin A. Lemkul ha
Francesca Vitalini wrote:
Actually the directory is of my own and I have created it in my home directory
so that shouldn't be a problem as I also have created other files in the same
directory without any problems so far.
Other ideas?
Thanks
Francesca
Il giorno 31/gen/2012, alle ore
On 31/01/2012 9:04 PM, Anik Sen wrote:
Hello,
Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job.
please help.
*The following is a part of the dna pdb file, which I am using:
*ATOM 1 O5' DG5 X 1 13.663 36.760 21.465 0.00
Thank you Justin for your quick reply. Unfortunately I cannot use a more modern
version of GROMACS as my topology and .gro files where first created for a
reverse transformation from cg to fg and thus required the 3.3.1 version and
some specific .itp files that are only present in that
Dear Gromacs specialists,
Can you help me about g_dist?
I have a micelle system, I want to obtain distance between center of mass of
micelle with the last of carbon bounded to head group in surfactant.
It should be near 2.2 but when I did g_dist -f md.xtc -s md.tpr -b 15 -o
dist.xvg and
I am replying to the Gromacs User's list rather than directly.
On Monday, January 30, 2012 12:38 AM,Tom dna...@gmail.comwrote:
Thanks for answering me my question and thanks for the nice open
source code program!
I found out my prvious problem due to the problem of my *mol2 file.
Can
Hi,
I suggest taking a look in RED.DB web site
(http://q4md-forcefieldtools.org/REDDB/index.php), where some RESP charges
for DNA are stored.
HTH
Stephane
--
Message: 1
Date: Tue, 31 Jan 2012 16:11:02 +1100
From: Mark
openSUSE 12.1 64bit.
I have managed to compile grogui with plotting on earlier versions of
openSUSE. However when I attempt compiling the program on my current OS
I get the following errors:
src/editor.cpp: In member function ‘void Editor::updateMenus()’:
src/editor.cpp:156:59: error: ‘class
Well I'm keeping struggling with this script. Apparently the problem in in
using the integrator md with the GOMACS 3.3.1 version. In fact the same
.mdp file with integrator steep works. while with md it always gives the
error message that it cannot open the .xtc file.
How can I get around this
francesca vitalini wrote:
Well I'm keeping struggling with this script. Apparently the problem in
in using the integrator md with the GOMACS 3.3.1 version. In fact the
same .mdp file with integrator steep works. while with md it always
gives the error message that it cannot open the .xtc
Hi, there
I would like to select, for example, CA of GLY, CB of PRO, so I typed r
GLY a CA | r PRO a CB, but it doesn't work. make_ndx also doesn't
support parenthesis, either.
Previously, I used r GLY a CA (save as group 1), then r PRO a CB
(save as group 2), then 1|2, and finally del 1,
Thanks for the explanation! Is the improper dihedral in GROMACS implemented
in an unsigned fashion?
On Mon, Jan 30, 2012 at 9:01 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 31/01/2012 2:59 PM, Li SUN wrote:
So please look at the attached figure which is exactly the leftmost
You should try this:
http://verahill.blogspot.com/2012/01/debian-testing-64-wheezy-compiling_20.html
2012/1/31 Efrat Exlrod efrat.exl...@biu.ac.il:
Hi,
I'm compiling gromacs 4.5.5 with gcc compiler (v 4.5.3), cmake (2.8.7) and
OpenMM 3.1.1 on Linux (Red Hat release 5.7). I have followed the
On 2012-01-31 19:49, Li SUN wrote:
Thanks for the explanation! Is the improper dihedral in GROMACS
implemented in an unsigned fashion?
Yes, that means that changing the order of atoms changes the sign and
this may give you the opposite chirality.
On Mon, Jan 30, 2012 at 9:01 PM, Mark
Hi Rene,
Thanks for your reply. One question though. How much overhead do you think
I would have in calling mdrun -rerun after every step and would it run
more efficiently if I used GromPy?
Thanks,
Gianluca
On Tue, 31 Jan 2012, Pool, R. wrote:
Hi Gianluca,
Ah, I get it. In that
Sorry for the delay, but I used gcc version 4.1.2 20080704 to compile
our version of GPU enabled gromacs.
Matt
On Sat, Jan 28, 2012 at 11:32 AM, Benjamin Hall
benjamin.a.h...@ucl.ac.uk wrote:
Justin A. Lemkul wrote:
We get junk output with 4.5.4 if the box size is set to zero, for some odd
I should add that while we had runs that completed, all we got were
NaN for the coordinates and energies.
Personally, I have attributed our inability to execute the GPU code
cleanly to our C2050 Teslas [they are double precision]. (As I had
the GPUized code working with an earlier card, although
An RDF is normalised to the density for the entire box, so you should simply be
using that.
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
On 1/02/2012 5:02 AM, Zhuyi Xue wrote:
Hi, there
I would like to select, for example, CA of GLY, CB of PRO, so I typed r
GLY a CA | r PRO a CB, but it doesn't work. make_ndx also doesn't
support parenthesis, either.
Previously, I used r GLY a CA (save as group 1), then r PRO a CB
(save
On 1/02/2012 1:05 AM, dina dusti wrote:
Dear Gromacs specialists,
Can you help me about g_dist?
I have a micelle system, I want to obtain distance between center of
mass of micelle with the last of carbon bounded to head group in
surfactant.
It should be near 2.2 but when I did g_dist -f
On 28/01/2012 7:09 AM, Alex Marshall wrote:
Hi all,
I was trying to extend my simulation but I used the wrong .tpr file
when I called mdrun_mpi. I didn't catch it in time and my checkpoint
files were overwritten. Now I've used GROMPP to extend the simulation
(as directed in
Thanks Mark!
On Tue, Jan 31, 2012 at 7:26 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 28/01/2012 7:09 AM, Alex Marshall wrote:
Hi all,
I was trying to extend my simulation but I used the wrong .tpr file when I
called mdrun_mpi. I didn't catch it in time and my checkpoint files were
Hello,
Am anik. Am using gromacs 4.5.5
But the dna.rtp file contains the atom bname N3 under the residue file DT. So
whats the problem then.
the dna.rtp file for DT
[ DT ]
[ atoms ]
P P 1.16590 1
O2 O1P -0.77610 2
O2 O2P
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 the last
carbon
On 1/02/2012 4:19 PM, Anik Sen wrote:
Hello,
Am anik. Am using gromacs 4.5.5
But the dna.rtp file contains the atom bname N3 under the residue file
DT. So whats the problem then.
Yes, that's the reason from the problem. Your input structure doesn't
have that... I said:
pdb2gmx can only
When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is
showing the following options:
0 System : 18379 atoms
1 Protein : 11739 atoms
2 Protein-H : 9135 atoms
3 C-alpha : 1173 atoms
4 Backbone: 3519 atoms
5
On 1/02/2012 4:26 PM, 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
On 1/02/2012 6:04 PM, Anushree Tripathi wrote:
When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is
showing the following options:
0 System : 18379 atoms
1 Protein : 11739 atoms
2 Protein-H : 9135 atoms
3 C-alpha : 1173
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:
;Include DPPC chain topology
#include dppc.itp
That's why I have found the atoms wich belongs to DPPC molecule from
dppc.itp file itself.
On Wed, Feb 1,
Thanks for your reply.
I looked at this guide but I still wonder - can't the deletion of instances of
-fexcess-precision=fast affect performance? And why is this flag unrecognized?
Thanks, Efrat
Date: Tue, 31 Jan 2012 21:50:53 +0300
From: ?? ?? gontc...@gmail.com
Subject: Re:
I dont know exactly, but yesterday I've installed gromacs with this
guide and now everything works fine.
2012/2/1 Efrat Exlrod efrat.exl...@biu.ac.il:
Thanks for your reply.
I looked at this guide but I still wonder - can't the deletion of instances
of -fexcess-precision=fast affect
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