On 4/27/2011 4:55 PM, ana johari wrote:
dear justin,
Hello,after 5ns MD,based on your recommend, I use" trjconv -f -s
-pbc -mol -center -o *.pdb" command to get the whole protein without
any separation,but I found some part of the residue was broken,and
some new bond at the end of some resid
Mark Abraham skrev 2011-04-27 03.01:
On 4/27/2011 5:13 AM, shivangi nangia wrote:
Dear gmx users,
I need to design a starting configuration of a polypeptide with
charged side chains sitting in a box of water with Cl- ions within 7
ang of its radius.
I realize that in such a system like char
On 4/27/2011 3:51 PM, Lipi Thukral wrote:
Hi Justin,
I am using Gromacs 4.5 beta-2.
gmxcheck with file 1 and file 2 tells me exactly the number of frames
I specified.
gmxcheck -f File1.xtc
Frames: 2175
gmxcheck -f File2.xtc
Frames: 1232
While after concatenating, it skips the frames and the
You could try
trjconv -f -s -pbc res -ur compact -center -o
Good luck.
Von: gmx-users-boun...@gromacs.org im Auftrag von ana johari
Gesendet: Mi 27.04.2011 08:55
An: gmx-users@gromacs.org
Betreff: [gmx-users] Fw: trjconv -pbc and broken reside
dear justin,
H
On 4/27/2011 4:02 PM, huzhongq...@gmail.com wrote:
Dear all,
This question does not address issues of GROMACS development, and so
does not belong on gmx-developers. Please direct queries to the
appropriate forum. I am replying on the gmx-users list.
I am calculating the interaction between A
dear users
is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, apart
from
each other and not being crystallized in the right place. can i omit them and
replace ADP's with MG-ATP? or I should introduce this topology to gromacs?
regards
sajad --
gmx-users mailing listgmx-use
Hi all
I want to simulate using GROMACS.Before I used LAMMPS but it has not
polarizable water models. Therefore I want to use GROMACS.
I need .itp and .mdp files of POL3 water model.
Do you have the files.
Would you please help me.
Thanks alot for your time and attention
Regards
Saly
--
gm
Dear Users
I read so many emails to mailing list, there were important notes about
docking but I couldn't extract a general result.
Please let me know:
1-Can we dock a ligand to it's protein's binding pocket with Pymol and
Gromacs as following?
first:locating ligand outside and close to binding
Hi.
Looking at the list of building blocks available in GROMACS
(http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks)
you can find ATP as well as MG. So having a ATP-MG-complex in your simulation
shouldn't be a problem.
Regards,
Felix
On 4/27/2011 6:52 PM, Sajad Ahrari wrote:
dear users
is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG,
apart from each other and not being crystallized in the right place.
can i omit them and replace ADP's with MG-ATP? or I should introduce
this topology to gromacs?
You'l
On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:
Dear Users
I read so many emails to mailing list, there were important notes
about docking but I couldn't extract a general result.
Please let me know:
1-Can we dock a ligand to it's protein's binding pocket with Pymol and
Gromacs as following?
Dear Saly
from my little experience, POL3 water model is a point polarizable
water model.
Point polarizable water models are not available in gromacs.
Gromacs uses shell model, i.e. charge attached on a spring to mimic the
stretching of the electronic cloud.
So you have 3 solutions
a) Yo
Dear Mark
Thank you for your reply.yes,you are right.
Regarding question 2:
I have a pdf file from "Docking Server" for sertraline-SERT example.Suppose
this is a good docked state.
In the other hand,I did what I explained in section 1 for sertraline and
SERT.(by pymol and ...)
Now, I want to chec
On 4/27/2011 7:52 PM, mohsen ramezanpour wrote:
Dear Mark
Thank you for your reply.yes,you are right.
Regarding question 2:
I have a pdf file from "Docking Server" for sertraline-SERT
example.Suppose this is a good docked state.
In the other hand,I did what I explained in section 1 for sertra
Sir,
I have copied database directories in my home directory by editing
.bashrc file ,still while using gromacs utilities its reading the database of
root .Is there any other changes i.e; if I have to give the path elsewhere so
that it should read the home copied database.
On 4/27/2011 8:24 PM, Prema Awati wrote:
Sir,
I have copied database directories in my home directory by
editing .bashrc file ,still while using gromacs utilities its reading
the database of root .Is there any other changes i.e; if I have to
give the path elsewhere so that it should re
Hi,
I was wondering if anyone new a way to run mdrun commands through a condor
system. I've been told by the people that run our system that unless I can
split it into seperate threads then I would not be able to run it as a job,
because it would just get stopped in the morning - which from wh
Dear David,
Dear Justin,
I have now installed the latest version of Gromacs 4.5.4. The problem still
persists.
The two files to concatenate do not have exactly the same timeframes.
However they do have something like the following:
File 1: 2091000.000
File 2: 2090170.000
May be I don't u
Lipi Thukral wrote:
Dear David,
Dear Justin,
I have now installed the latest version of Gromacs 4.5.4. The problem
still persists.
The two files to concatenate do not have exactly the same timeframes.
However they do have something like the following:
File 1: 2091000.000
File 2: 20901
Work with your condor people to recompile gromacs against MPI on their system,
if that is not already the case.
It's probably helpful to specify +ParallelShutdownPolicy = "WAIT_FOR_ALL"
in the condor submission file...
See http://www.cs.wisc.edu/condor/manual/v7.6/2_9Parallel_Applications.html
Sect
On 4/27/2011 9:40 PM, Lipi Thukral wrote:
Dear David,
Dear Justin,
I have now installed the latest version of Gromacs 4.5.4. The problem
still persists.
The two files to concatenate do not have exactly the same timeframes.
However they do have something like the following:
File 1: 2091000.00
On 4/27/2011 9:08 PM, Natalie Stephenson wrote:
Hi,
I was wondering if anyone new a way to run mdrun commands through a
condor system. I've been told by the people that run our system that
unless I can split it into seperate threads then I would not be able
to run it as a job, because it woul
P, I'm afraid :-) Pretty much anything that has
> been done can be made to work in GROMACS, however.
>
> See also http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> Mark
>
>
>
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On 4/27/2011 10:08 PM, saly jackson wrote:
Hi Ivan
Please do not reply to whole digests with non-descriptive subject lines.
It confuses the archives, and alienates people from finding out the
topic of your interest, and thus being bothered to give you free help.
Please leave only the releva
l: +420775504164
e-mail: ivan.glad...@uochb.cas.cz <mailto:ivan.glad...@uochb.cas.cz>
web page:http://www.molecular.cz/~gladich/
<http://www.molecular.cz/%7Egladich/>
-
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Before making a MD simulation you should try to
explore different ways to analyze your docking results. For example, performing
the same experiment with different docking programs and scoring functions
(“consensus
scoring”) and compare the results, is there consistency between them?. Now, if
docki
Dear gmx-users,
since I'm sending my simulations to a system with a queue with a wallclock
time of 24 h, I necessarily have to simulate small parts of my simulation,
that I "stick" together at the end with trjconv. To continue my simulations,
I'm using the .cpt file. Here my settings concerning the
Anna Marabotti wrote:
Dear gmx-users,
since I'm sending my simulations to a system with a queue with a
wallclock time of 24 h, I necessarily have to simulate small parts of my
simulation, that I "stick" together at the end with trjconv. To continue
my simulations, I'm using the .cpt file. He
Justin A. Lemkul wrote:
It is possible this is a bug related to nst*out/energy/log being writing
every 5 steps and assuming init_step = 0 (i.e. writing at 100 ps
rather than 240 ps, based on your initial settings). What version of
Gromacs is this?
Actually, this wouldn't be considered
Hi all
I want to know about the ability of GROMACS to simulate sulfate in(SO4
(2-)),
Do we can have the ion in our simulation using GROMACS?
Thanks alot
Saly
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
htt
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Message: 4
Date: Wed, 27 Apr 2011 08:24:52 +0200
From: David van der Spoel
Subject
saly jackson wrote:
Hi all
I want to know about the ability of GROMACS to simulate sulfate in(SO4
(2-)),
Do we can have the ion in our simulation using GROMACS?
That depends on the force field you want to use. There are parameters for
sulfate in all of the Gromos force fields, but I ca
On 2011-04-27 17.58, Xiaohu Li wrote:
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Message: 4
Date: Wed, 27 Apr 2011 08:24:52
Dear Mark Abraham & all,
We used another benchmarking systems, such as d.dppc on 4 processors,
but we have the same problem (1 proc use about 100%, the others 0%).
After for a while we receive the following error:
Working directory is /localuser/armen/d.dppc
Running on host wn1.ysu-cluster.gr
This seems to be a problem with your MPI library. Test to see whether other
MPI programs don't have the same problem. If it is not GROMACS specific
please ask on the mailinglist of your MPI library. If it only happens with
GROMACS be more specific about what your setup is (what MPI library, what
ha
Dear Roland,
We need to run the GROMACS on the base of the nodes of our cluster (in
order to use all computational resources of the cluster), that's why we
need MPI (instead of using thread or OpenMP within the SMP node).
I can run simple MPI examples, so I guess the problem on the
implementat
On 4/28/2011 4:44 AM, Hrachya Astsatryan wrote:
Dear Roland,
We need to run the GROMACS on the base of the nodes of our cluster (in
order to use all computational resources of the cluster), that's why
we need MPI (instead of using thread or OpenMP within the SMP node).
I can run simple MPI exa
Hi Mark,
I am excited to see that there is a solution to my issue. I thought this
problem can not be resolved.
In thermodynamics of polymer solutions, people use some models (equation of
state) in which an interaction parameter K_AB appears which is defined in
terms of interaction energies i.e. 1
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the molecule only
has non-bonding interaction but there was no intramolecular motion
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule, it is mentioned that it has been used as 'rigid' molecule i.e
the molecule only has non-bonding interaction but there was no
i
On 4/28/2011 11:25 AM, Justin A. Lemkul wrote:
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule, it is mentioned that it has been used as 'rigid' molecule
i.e the molecule only
Thanks. The molecule was developed as a part of OPLS. The authors used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases, j
On 4/28/2011 10:06 AM, Elisabeth wrote:
Hi Mark,
I am excited to see that there is a solution to my issue. I thought
this problem can not be resolved.
In thermodynamics of polymer solutions, people use some models
(equation of state) in which an interaction parameter K_AB appears
which is d
Hi,
I tried to keep the geometry of the BF4 fixed by using constraints using
lincs. But , unfortunately, my simulation is crashing immediately and if I try
minimization with only 2 molecules, it provides a lot of LINCS warning and
generate a lot of step*.pdb file . If I try to visualize the mi
On 4/28/2011 1:54 PM, Sanku M wrote:
Hi,
I tried to keep the geometry of the BF4 fixed by using constraints
using lincs. But , unfortunately, my simulation is crashing
immediately and if I try minimization with only 2 molecules, it
provides a lot of LINCS warning and generate a lot of step*.
Hi there,
I am trying to install gromacs-4.5.4 on my local machine with FC, I tried
following set of commands:
-to install FFTW at location
root/Desktop/Vivek/calcitonin/FFTW
./configure --prefix=/root/Desktop/Vivek/calcitonin/FFTW
--enable-long-double
make
make install
vivek sharma wrote:
Hi there,
I am trying to install gromacs-4.5.4 on my local machine with FC, I
tried following set of commands:
-to install FFTW at location
root/Desktop/Vivek/calcitonin/FFTW
./configure --prefix=/root/Desktop/Vivek/calcitonin/FFTW
--enable-l
On 4/28/2011 2:52 PM, vivek sharma wrote:
Hi there,
I am trying to install gromacs-4.5.4 on my local machine with FC, I
tried following set of commands:
-to install FFTW at location
root/Desktop/Vivek/calcitonin/FFTW
./configure --prefix=/root/Desktop/Vivek/calcito
Hello Users,
I have a query regarding simulation with the ligand.
In my protein there are two ligands, one of them (coenzyme) is from the
crystal data, and other I have docked at the active site, while docking
it is showing good interaction with all the active site residues very
well.
I used GROM
I went through the LINCS manual . But, I am still struggling with coming up
with the idea of putting correct constraint to maintain the rigidity of
tetrahedral molecule . I seem to understand from your suggestion that the
tetrahedral can be seen as a combination of 4 coupled triangles.( or
onetwo wrote:
Hello Users,
I have a query regarding simulation with the ligand.
In my protein there are two ligands, one of them (coenzyme) is from the
crystal data, and other I have docked at the active site, while docking
it is showing good interaction with all the active site residues very
On 4/28/2011 3:49 PM, Sanku M wrote:
I went through the LINCS manual . But, I am still struggling with
coming up with the idea of putting correct constraint to maintain the
rigidity of tetrahedral molecule . I seem to understand from your
suggestion that the tetrahedral can be seen as a com
On 4/28/2011 3:21 PM, onetwo wrote:
Hello Users,
I have a query regarding simulation with the ligand.
In my protein there are two ligands, one of them (coenzyme) is from the
crystal data, and other I have docked at the active site, while docking
it is showing good interaction with all the activ
Dear Aldo
Thank you for your reply
Mark's notes and yours were very useful.
Best
mohsen
On Wed, Apr 27, 2011 at 6:46 PM, Aldo Segura wrote:
> Before making a MD simulation you should try to explore different ways to
> analyze your docking results. For example, performing the same experiment
> w
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