Hi.
I'm trying to subject a metalloprotein bound to cadmium to a molecular
dynamics. I've defined the cadmium ion in the atom type parameter file
(ffGa56a6.atp) and residue database (ffG53a6.rtp). And the bond length and
bond angle between the cadmium and sulphur of the metalloprotein had been
Amin,
maybe your MPI-enabled executable is called mdrun_mpi. Check
the directory where mdrun is and make shure (with ldd for example)
the mdrun* you are using is linked to the MPI library you are using.
Carsten
On Jun 24, 2010, at 6:51 AM, Amin Arabbagheri wrote:
Carsten,
Thanks for your
Ni hao Kwee Hong,
These special links should be defined in the file specbond.dat. That
file you can find in the gromacs topology data directory. Have a look
at the linkage of iron, e.g.. Also check the manual/wiki/mailinglist
on 'specbond.dat' for more information.
Hope it helps,
Tsjerk
On
Dear users,
I have a question about vdwtype. My question is if I use vdwtype=shift in
nvt.mdp file:
; Neighborsearchingns_type = grid ; search neighboring
grid celsnstlist = 5 ; 10 fsrlist= 1.0
; short-range neighborlist cutoff
you zou skrev:
Dear users,
I have a question about vdwtype. My question is if I use vdwtype=shift
in nvt.mdp file:
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range
Dear GROMACS team members,
I have a general question about the GROMACS, actually I have used GROMACS
for the simulation of 59 amino acids domain part of the protein
containing within it. This domain lies in the position from 34-92 out of 239
residues, this loop having only 12 residues similarity
onetwo wrote:
Thanks Justin for the help,
I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.
Mangnese may have topology similar to Magnesium 2+, What I found is that
Assuming a transition metal may be similar to another species
pawan raghav wrote:
Dear GROMACS team members,
I have a general question about the GROMACS, actually I have used
GROMACS for the simulation of 59 amino acids domain part of the protein
containing within it. This domain lies in the position from 34-92 out of
239 residues, this loop having
Dear GMX-users,
This is Justin.
I am performing coarse-grained simulation on a protein-lipid bilayer system.
This is a MARTINI CG model.
I have successfully completed a 360ns simulation, during which the time step
is 30 fs.
I would like to extend the simulation to 1micro-second. The commands I
Dear All,
I've been trying to compile and get Gromacs (version 4.0.7) working on a
cluster that runs with Debian Lenny.
I set the following variables:
export SOFT=$HOME/GROMACS
export PATH=$PATH:$SOFT/bin
export LDFLAGS=-L$SOFT/lib
export CPPFLAGS=-I$SOFT/include
export
I am trying to create a .gro file of a single detergent which I am going to
then multiply and put it in water and have it form micelles. In order to create
a .gro file, I know I need to create a .rtp file of my residue or add it to the
desired force field .rtp file I want to run my detergent
Hi everyone,
please I'm doing for the first time a covariance analysis.
I followed this tutorial:
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.htmlhttp://nmr.chem.uu.nl/%7Etsjerk/course/molmod/analysis1.html
But I don't understand. -proj gives the projection of the trajectory on the
Amanda Watkins wrote:
I am trying to create a .gro file of a single detergent which I am going
to then multiply and put it in water and have it form micelles. In order
to create a .gro file, I know I need to create a .rtp file of my residue
You do not *need* a .gro file, nor do you
Hi All,
I'm trying to use g_sorient to calculate some solvent properties in a few
systems I'm simulating. It's the first time I've used the tool, so if I've
missed something obvious, please let me know. I'm getting a very weird error
when I execute the command:
echo 1 13 |
Dear gmx users,
I am trying to calculate the Van Hove correlation function (G(r,t))
using the utility g_vanhove. However, I don't seem to be able to make it
work. The program outputs files, but the points are all 0 except at r=0.
My simulation is a hydrated lipid bilayer with 128 molecules. I
Hi Chris. Thanks for getting back to me. My problem is with the conversion to
standard state concentration (1M) from umbrella sampling simulations. I can't
understand how to do this from my umbrella sampling simulations. Even after
reading several papers that perform the correction unclear on
section 7.3.11 of gromacs manual (v4.0)/
-Gaurav
On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund er...@xray.bmc.uu.se wrote:
you zou skrev:
Dear users,
I have a question about vdwtype. My question is if I use vdwtype=shift in
nvt.mdp file:
; Neighborsearching
ns_type = grid ; search
- Original Message -
From: Christian Mücksch mueck...@rhrk.uni-kl.de
Date: Friday, June 25, 2010 0:21
Subject: [gmx-users] Problems with installing mpi-version of Gromacs on Cluster
with Debian-Lenny
To: MAILINGLIST GROMACS gmx-users@gromacs.org
Dear All,
I've been trying to
Dear Elio:
I think I was pretty clear in my last email:
If you still have trouble, then your next post should include things
like I tried this... but I didn't understand this specific part
to make it clear that you have put in the effort here.
Otherwise, hopefully somebody else has the
How about using the last .gro file to continue your simulation?
2010/6/24 张春雷 chunleizhang@gmail.com
Dear GMX-users,
This is Justin.
I am performing coarse-grained simulation on a protein-lipid bilayer
system. This is a MARTINI CG model.
I have successfully completed a 360ns
Thank you for your help friends, But I have no any idea about amount of
rvdw-switch. I would like to use vdwtype=shift(shift LJ to 0), but I don't know
which number for rvdw-switch and rvdw should be choice? In manual I saw
rvdw-switch=0 and rvdw=1.0, but it had this error. section 7.3.11 of
Dear gromacs users,
I have been trying to use a polymer in the system and for its topology
generation I have created its .rtp file. I am having trouble using the .rtp
file in pdb2gmx command as it shows file input/output error. Can anyone
please help me as to how i should use the .rtp file in
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