On 07/05/2012 01:04 PM, SatyaK wrote:
Thanks once again Mark. I am trying to figure out things. Basically, I am
using ReaxFF for my simulations.
Has that been ported to GROMACS? If not, you have that issue to consider
first.
The basic problem I want to address is, to
place OH radicals
Dear GROMACS Users,
I'm planning to work on a protein that activates itself under lower pH
conditions. And I don't have any clues how to do it in GROMACS. My first
question is about the possibilities to do this in GROMACS, has anyone done
this before? It can even be a constant simulations at a
Dear Peterson,
There's no magic wand for this. You'll need to find out pKa values of
titrable amino acids in your protein (in literature, MEAD software,
etc.). Then, you can protonate (pHpKa) / deprotonate (pHpKa) those
group according to the pH.
-G
On Thu, Jul 5, 2012 at 12:33 PM, J Peterson
Hi Satya,
You can use trjorder to rearrange solvent molecules in your structure
file, according to distance. Then you can replace the first x solvent
molecules by hydroxyl. Actually you only need to remove a hydrogen
atom per water...
Hope it helps,
Tsjerk
On Thu, Jul 5, 2012 at 5:04 AM,
On 07/05/2012 05:03 PM, J Peterson wrote:
Dear GROMACS Users,
I'm planning to work on a protein that activates itself under lower pH
conditions. And I don't have any clues how to do it in GROMACS. My first
question is about the possibilities to do this in GROMACS, has anyone done
this before?
Thanks Tsjerk for your guidance. In fact, I had been removing some H atoms
from the water molecules (which are close to DNA by choosing them manually
depending on the coordinates which is a tedious process) to convert them to
OH. Then, I try to input this file to Lammps applying Reaxff
Hello Tsjerk,
I was wondering, once we order the water molecules and place Oh radicals in
the system, do we loose the continuity of their trajectories when we run
the simulations using Lammps?
With Regards,
Satya.
--
View this message in context:
Uhmm, you remove particles, modify molecule types, and wonder whether
there is continuity in the trajectories?
Ah well, let's say you were to do a simulation and at some point t you
suddenly have some hydrogen atoms that have lost all interaction with
the system, and on top of that have the
Hi all,
:
A quick question here:
Does the g_msd program (v4.5.5) take into account the finite size
effect due to PBC when it computes/gives translational diffusion ?
sa
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text
I am trying to implement dihedral restraints for lipids in a bilayer
using what is suggested here:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
However, although the dihedral angles seem to be restrained fine, the
leaflets move apart by 10s of nanometers along +z over a
On 7/5/12 10:25 AM, himanshu khandelia wrote:
I am trying to implement dihedral restraints for lipids in a bilayer
using what is suggested here:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
However, although the dihedral angles seem to be restrained fine, the
leaflets
Hi everybody,
I want to minimize the energy of my structure.
I use the following mdp file:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 5000
nstenergy = 1
energygrps = System
coulombtype = PME
On 2012-07-05 16:23, sa wrote:
Hi all,
:
A quick question here:
Does the g_msd program (v4.5.5) take into account the finite size
effect due to PBC when it computes/gives translational diffusion ?
sa
yes.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol.,
On 7/5/12 10:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to minimize the energy of my structure.
I use the following mdp file:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 5000
nstenergy
In June 2005 Berk Hess wrote (in this list):
Determining ionic solvation free energies is very tricky business,
experimentally as well as theoretically.
Last week I heard a talk by P. H. Hünenberger who explained
all the proper corrections you need to make for different electrostatics
Dear All,
So I am using some scripts to parse through 100s of files using bash and awk.
In any case, I run into a problem as follows; I have Ubuntu at home on my PC
and I have a laptop at work with Ubuntu, same versions libraries, everything.
When I run the scripts at home they work fine,
Dear gmx-people.
I know that if you send a KILL signal do a mdrun instance running
integrator = md it sets nsteps to the next NS step and exits
gracefully, but I don't see it happening to minimization runs.
Is it possible to send a signal ta minimization instance of mdrun to
make it exit as if
Hi all!
I am trying to set up hemoglobin simulations using GROMOS96 53a6 force
field. pdb2gmx runs without errors, however, topology file does not have
the His-Fe bond type, etc.
Does someone have detailed step-by-step instructions of how to prepare oxy- and
deoxy-Hb for gromacs simulations?
Hi,
you might want to try the following code in bash
#!/bin/bash
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_$i.edr -o $i.xvg EOF
i=`expr $i + 1`
done
Hope this helps!
Shounak
lloyd riggs wrote
Dear All,
So I am using some scripts to parse through 100s of files using bash and
Hi,
I'm new to gromacs, after following a few lectures on MD decided to try out
this gromacs tutorial:
http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html
http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html
I can get till the section Energy minimization of the solvated system but
then I get an
Hi,
you might want to try the following code in bash.
I do not know if you specifically need to create a here-document
#!/bin/bash
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_$i.edr -o $i.xvg
i=`expr $i + 1`
done
Hope this helps!
Shounak
lloyd riggs wrote
Dear All,
So I am using
On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
Does any one know why, or have some other scripts...
My suggestion would be something in the lines of
#!/bin/bash
for i in $(seq 2121) ; do
g_energy -f traj_${i}.edr -o ${i}.xvg ${i} 0
done
===
Notice the in keyword
On 7/5/12 3:15 PM, jonas87 wrote:
Chopping out a bunch of unnecessary stuff...
*editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
1.0 *
Read 1202 atoms
No velocities found
system size : 5.245 4.320 2.507 (nm)
diameter: 5.532 (nm)
I'm following the tutorial exactly. Even have my files named the same way.
The contents of my minil.mdp (pcb is changed from no to xyz right before
running the energy minimazation of the solvated system):
title = Energy Minimization ; Title of run
cpp = /lib/cpp ;
On 7/5/12 5:05 PM, jonas87 wrote:
I'm following the tutorial exactly. Even have my files named the same way.
The contents of my minil.mdp (pcb is changed from no to xyz right before
running the energy minimazation of the solvated system):
title = Energy Minimization ; Title of run
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_x.edr -o ${i}.xvg EOF
${i}
EOF
i=$(($i+1))
done
Still can not figure out the difference, or why one works on one PC and not the
other?
Stephan (in Rainy
Protein-water.pdb has the following line:
CRYST1 75.324 75.324 75.324 60.00 60.00 90.00 P 1 1
But after adding the NA/CL ions with genion the CRYST1 line is missing
entirely from the output file protein-solvated.pdb
Could this be because of the bug u mentioned?
I'm using the
On 7/5/12 5:51 PM, jonas87 wrote:
Protein-water.pdb has the following line:
CRYST1 75.324 75.324 75.324 60.00 60.00 90.00 P 1 1
But after adding the NA/CL ions with genion the CRYST1 line is missing
entirely from the output file protein-solvated.pdb
Could this be because of
On 6/07/2012 7:25 AM, lloyd riggs wrote:
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_x.edr -o ${i}.xvg EOF
${i}
EOF
i=$(($i+1))
done
Still can not figure out the difference, or why one works on one PC and
On 6/07/2012 2:46 AM, Elton Carvalho wrote:
Dear gmx-people.
I know that if you send a KILL signal do a mdrun instance running
integrator = md it sets nsteps to the next NS step and exits
gracefully, but I don't see it happening to minimization runs.
Is it possible to send a signal ta
Hello Tsjerk,
I followed below steps to create a box with DNA and water molecules that
are close to it at some distance:
1. g_select -s Test.gro -select 'Close to A resname SOL and within 0.5 of
resname A' -on
(since I need around DNA molecule, I randomly chose residue A, such that
water
I am trying to implement dihedral restraints for lipids in a bilayer
using what is suggested here:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
However, although the dihedral angles seem to be restrained fine, the
leaflets move apart by 10s of nanometers along +z over a
Hey,
I'd probably go for something like:
for ((i=1; i...; i++)); do echo $i 0 | g_energy ...; done
Note the additional 0 to make g_energy exit. The (( )) has been in
bash for ages, so that shouldn't be a problem.
I notice that in the working construct you used 'traj_x.edr', while in
the
Hi,
Indeed, it's the 'box-gets-lost-bug'. It happens with the tutorial
because it was written for an earlier gromacs version. There's an
updated one for 4.5.5 at http://md.chem.rug.nl/~mdcourse/molmod2012/
Although I'll check again if that bug may still cause problems... If
you stick to .gro
Dear Gromacs users!
I have some problems with the simulation of protein-ligand complex
embedded in the ccl4-water environment. In addition there are some
crystallography waters (xw) embedded in the protein interiour of the
protein. I've done equilibration and minimisation of my system and run
it
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