Hello all
I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)
I am geeting error during addiotion of ions
Fatal error:
Your solvent group size (12548) is not a multiple of 3
For more information and tips for troubleshooting, please check the GROMACS
website at
Dear gromacs users
In a recent paper I found the following protocol of a gromacs simulation:
All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the
On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap sang...@imtech.res.inwrote:
Hello all
I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)
I am geeting error during addiotion of ions
Fatal error:
Your solvent group size (12548) is not a multiple of 3
For more information and
Dear Gmx Users,
Many of you probably faced an error:
An input file contains a line longer than 4095 characters, while the buffer
passed to fgets2 has size 4095. The line starts with: '20s'
As I noted this error comes from the changes in the topology. Gromacs somehow
add _ and thus this
On Fri, 2012-05-11 at 10:23 +0200, Bernhard Knapp wrote:
Dear gromacs users
In a recent paper I found the following protocol of a gromacs simulation:
All simulations were performed with the GROMACS 4.0 [12] compiled in
single-precision mode at a constant temperature of 277 K in a
I have a fully fluorinated alkane, and am wondering how to choose the right
atom-to-bead mapping. 4 CH2 groups form a C1 bead in Martini. Will CF2-CF2
(6 heavy atoms), also map to a C1 bead type? How does one go about making
the right choice?
Any suggestions will be so welcome
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Maria G.
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Dear Gromacs Users,
Is there any way in Gromacs which will allow me to contraint some of the
atoms in the system to move only in the coordinate X and Z? I do not want
some of my atoms to move in Y direction. Do you know how to do this?
Steven
--
gmx-users mailing listgmx-users@gromacs.org
11 maj 2012 kl. 14.38 skrev Steven Neumann:
Dear Gromacs Users,
Is there any way in Gromacs which will allow me to contraint some of the
atoms in the system to move only in the coordinate X and Z? I do not want
some of my atoms to move in Y direction. Do you know how to do this?
Hi,
Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work.
I was trying to run the dynamics for some inorganic metal halides
solvation in water. A fatal error is comingthat:
* Atomtype CH2r not found.
But in my system I have no such atoms. Only water molecules with tip4p model
You should paste your topology for you metal halides so that others can
help.
On Fri, May 11, 2012 at 9:48 PM, Anik Sen anik...@csmcri.org wrote:
Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work.
I was trying to run the dynamics for some inorganic metal
halides
Dear gmx users,
I'm going to simulate the POPC in water.
I downloaded required files in Tielman site and made the .top file. Then
included the CHARMM27.ff in the .top file.
When I run the grompp I get the fatal error as below:
Atomtype CB not found
I have done the same with gromos87.ff . But I
Dear Anik,
Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work.
Is there a particular reason you are using such an old version of
gromacs?
If not then switch to the latest version as there have been many
improvements
I was trying to run the dynamics for some inorganic
Dear Gromacs Users,
I created my own residues in aminoacids.rtp which each is formed of one
atom. I would like to somehow create bonds between then using standart
harmonic potential. Could you please advise how to do this?
Stevem
--
gmx-users mailing listgmx-users@gromacs.org
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using
mpirun and gives proper output. But whenever I try to submit it on
On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Dear gmx users,
I'm going to simulate the POPC in water.
I downloaded required files in Tielman site and made the .top file. Then
included the CHARMM27.ff in the .top file.
When I run the grompp I get the fatal
here is a simple example (for more complex ones see the existing
residues in an aminoacids.rtp)
assume molecule looks like
A-B-C
where the -'s are bonds
with residues AAA, BBB, CCC containing the corresponding atoms,
then the .rtp should contain something like:
[ AAA ]
[ atoms ]
A typeA
On Fri, May 11, 2012 at 9:10 PM, Anirban reach.anirban.gh...@gmail.comwrote:
On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh
shima_arasteh2...@yahoo.com wrote:
Dear gmx users,
I'm going to simulate the POPC in water.
I downloaded required files in Tielman site and made the .top file.
Dear Anirban,
No, I have not done. Because I didn't know I need Berger lipids for this
simulation.
Thanks for you reply,
Cheers,
Shima
From: Anirban reach.anirban.gh...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
All right.
Thank you
From: Anirban reach.anirban.gh...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Friday, May 11, 2012 8:11 PM
Subject: Re: [gmx-users] Simulation of POPC in water
Well, impressive explanation! Thank you very much!
Steven
On Fri, May 11, 2012 at 4:38 PM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
here is a simple example (for more complex ones see the existing
residues in an aminoacids.rtp)
assume molecule looks like
A-B-C
where
Dear Gromacs user,
I'm trying to calculate de distances between residues in a trajectory with
g_mdmat and I'm coming across a problem while trying to restrict only to a
smaller number of residues providing an index file. in fact what I get is a
matrix as big as if I use all the residues, and the
CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good
output of simulation.
Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36.
But about the atom types, it's not still clear for me what I need to do. If I
use the CHARMM36, am I supposed to build
On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a
good output of simulation.
Before this, Justin also suggested me for CHARMM36. Ok, I will use
CHARMM36. But about the atom types, it's
OK, I'll give it a try.
Thank you again! :-)
Cheers,
Shima
From: Anirban reach.anirban.gh...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Friday, May 11, 2012 9:22 PM
Subject: Re:
Hi,
as an alternative of applying position restraints to only the y-component,
one can also define a freeze-group only to act on the Y-axis by using:
freezedim N Y N
see: http://manual.gromacs.org/online/mdp_opt.html#neq freezegrps and freezedim
Oliver
On Fri, May 11, 2012 at 7:39 AM, Erik
Hi Guys
Could some one please let me know how to convert general amber force field bond
force constents to GROMACS bong function 1 type.
Thanks so much
Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA--
gmx-users mailing
On 5/11/12 3:54 PM, Milinda Samaraweera wrote:
Hi Guys
Could some one please let me know how to convert general amber force field bond
force constents to GROMACS bong function 1 type.
Bond type 1 is a simple harmonic bond. You need an equilibrium length and force
constant in appropriate
Hi,
Is there any tool in gromacs that can compute the fraction of native contacts
rho ( i,e the typical parameter that quantifies how close the folding
protein is to the native ) ?
Thanks
Sanku--
gmx-users mailing listgmx-users@gromacs.org
Hi,
Can anyone please tell me what is the difference between the commands
editconf and g_editconf? If there is no difference then why do some systems
recognize g_editconf but not editconf?
--
Regards,
Nitin Agrawal,
Master's Student (Bioinformatics)
University of Turku,Finland
B.Tech
On 5/11/12 7:40 PM, Nitin Agrawal wrote:
Hi,
Can anyone please tell me what is the difference between the commands editconf
and g_editconf? If there is no difference then why do some systems recognize
g_editconf but not editconf?
There is no difference. g_editconf is just editconf but
Thank you for your clarification.
On Sat, May 12, 2012 at 2:51 AM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/11/12 7:40 PM, Nitin Agrawal wrote:
Hi,
Can anyone please tell me what is the difference between the commands
editconf
and g_editconf? If there is no difference then why do
Dear gmx users,
Anybody can guide me to some articles which introduces CHARMM36 forcefield? I
want to study about this forcefield.
Thanks in advance,
Shima
From: Anirban reach.anirban.gh...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion
I would say looking at the CHARMM force field website would be the first thing
to do. Google: CHARMM FORCE FIELD, and you should get the relevant pages... The
articles are listed on the website...
/Jesper
On May 11, 2012, at 9:19 PM, Shima Arasteh wrote:
Dear gmx users,
Anybody can guide
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