Are you running NVT with position restraint dynamics of your protein?
Your system is probably not minimizied enough.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thu
Those tutorials show most important things (e.g. how to build topology for
given system) in CG Martini ff using Gromacs. You do not have to merge
anything. Commands are the same as for atomistic simulations
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
Jan
_
For MARTINI force field:
http://md.chem.rug.nl/cgmartini/index.php/tutorial
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of J Peterson [think_bey...@aol.com]
Sent: Monday, August 06, 2012 6:41 AM
To: gmx-users@gromacs
You can use editconf -princ to orient it into the principal axis. Then with
editconf -rotate specify proper vector of 90 degrees if required.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Abed Askari [abedask...@yah
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Marzinek, Jan [j.marzine...@imperial.ac.uk]
Sent: Wednesday, June 20, 2012 10:30 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraints
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Anik Sen [anik...@csmcri.org]
Sent: Wednesday, June 20, 2012 10:20 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraints
Dear Mark,
In
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Anik Sen [anik...@csmcri.org]
Sent: Wednesday, June 20, 2012 8:24 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraint
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Seera Suryanarayana [paluso...@gmail.com]
Sent: Friday, May 25, 2012 6:23 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error
Dear all gromacs users,
Hi Fabian,
The tpi integrator will caluclate it for you when you simply add the extra
molecule to your gro and topology:
http://www.mail-archive.com/gmx-users@gromacs.org/msg50610.html
Best,
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@
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
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Krzysztof Kuczera [kkucz...@ku.edu]
Sent: Wednesday, May 02, 2012 6:38 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] pullf.xvg
Could someone please tell me
But the best would be to grompp (NPT) windows (lets say every 10-20 frames) of
your configuration and at the end of grompp you will see the actual distance
the gromacs will consider.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on beh
Use trjconv -skip first for your trajcetory so you can rewrite it every
frame/time step you want. Then proceed to g_dist.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Shilpi Chaurasia [shilpi.chaura...@unimi.it]
Sent: Mon
From: Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thursday, April 12, 2012 4:53 PM
To: Marzinek, Jan
Subject: Re: [gmx-users] Gromos87
Dear Jan,
I downloaded the file and put it in my working space but does not appear in my
force filed selections? How
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thursday, April 12, 2012 4:05 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Gromos87
Dear friends,
I'd like to use g
Well... There is no mistake as for the option -t of grompp in the suggested
version for this tutorial the file can be both trajcetory (trr) or a checkpoint
file (cpt) from previous NVT ensemble. I hope you understand what you are doing?
Jan
From: gmx-users-
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Lara Bunte [lara.bu...@yahoo.de]
Sent: Monday, March 05, 2012 5:24 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] em.mdp file
Hello
Is this em.mdp file correct for a sim
try:
$ df -h .
And see how much quota you have available.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of RAMYA NAGA [nagra...@gmail.com]
Sent: Wednesday, February 29, 2012 8:28 AM
To: Discussion list for GROMACS user
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
Re
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
So as you can see Gromacs does not support multi file input :) Create one index
file and specify there your two groups. Then g_hbond will ask you to choose two
groups from this file.
Jan
===
Jan Marzinek
PhD Candidate
Centre for Proce
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of lina [lina.lastn...@gmail.com]
Sent: Thursday, October 27, 2011 10:47 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] trjconv and -pbc
Hi,
I have a problem usi
Dear Gromacs Users,
I used PRODRG server in order to obtain the topology file for my molecule (52
atoms with all hydrogens). However, server generated Gromacs topology which
involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will
use the pdb file with missing 4 hydrogen
Dear Gromacs Users,
As I know for the Energy Minimization algorithms both Steepest Descent and
Conjugate Gradient will not provide a global minimum of the potential energy
but only a local minium.
Does anyone know how Gromacs choose the starting point on the potential energy
hypersurface for th
Marzinek, Jan wrote:
> Dear Justin,
>
> Thank you for the link! I know how to calculate it - that is what I am doing.
> Interface AREA = 0.5 (Protein SAS+ 30 Ligands SAS- Protein and 30Ligands
> SAS) This is relevant to the situation where ligands do not aggregate.
>
> I my system
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Tuesday, July 05, 2011 12:45 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SAS of ligands
Marzinek, Jan wrote:
> Dear Gromacs Us
Dear Gromacs Users,
My system has 30 ligands - they aggregate and and seperate during the
simulation time and stack to two sites of my protein (two clusters). I want to
calculate the interface area between ligands and protein so I need to substract
the interface between ligands due to the agg
Dear Gromacs Users,
I am running the simualtions between ligands (10-30) and protein - coiled coil
segment. My ligand is strongly hydrophobic and the hydrohpohobic strand between
two monomers is obviously hidden. I found that my proetin is unfloding from
terminals, two strands open allowing l
Dear Gromacs Users,
I am calculating the hydrophobic interface area using g_sas between ligands
(their hydrophobic solvent accessible surface area (SASA) >95%) and hydrophobic
residues of coiled coil fragment of protein (two helical strands) as follows:
Protein SASA + ligand SASA - Protein&Liga
Hi,
I have a question related to the calculation of hydrogen bonds in Gromacs. As I
read in Manual it comes from the distance between donor and acceptor ( <= 0.35
nm) and the angle <=30 degr beween hydrogen and acceptor. The question is - why
30 degr? How is it related to the reality?
The
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