> Thanks for you reply but, I'm afraid it doesn't work with me!
>
> In fact, if I write "more \#conf.gro#" I can read from this file.
>
> However, when using it as input for gromacs utilities the programs
> complain
> of input error.
cp #conf.gro# good.gro
___
Thanks for you reply but, I'm afraid it doesn't work with me!
In fact, if I write "more \#conf.gro#" I can read from this file.
However, when using it as input for gromacs utilities the programs complain
of input error.
Pedro.
2007/3/16, Mark Abraham <[EMAIL PROTECTED]>:
> Hi,
>
> maybe this
> Hi,
>
> maybe this is a linux-related question (sorry!) but how do I read from the
> backup files, such as #ener.edr# or #traj.xtc#?
The same way you do any other file. :-) You can even give them as input to
gromacs utilities.
Mark
___
gmx-users mai
Hi,
maybe this is a linux-related question (sorry!) but how do I read from the
backup files, such as #ener.edr# or #traj.xtc#?
Regards,
Pedro.
___
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http://www.gromacs.org/mailman/listinfo/gmx-users
Pleas
OK, further info on this. Looks like it's the minimizer, at least in
the case of freeze groups. I'm using l-bfgs; it seems the minimizer
doesn't respect the constraints imposed by freeze groups.
Now that I think of it, I seem to remember that most of the minimizers
in GROMACS don't respect constr
If they are at the carbon-carbon bond distance, then their van der
Waals radii will be overlapping and the force between them is huge.
You can turn off this interaction with energygrp_excl = atom1 atom2
(with atom1 and atom2 defined in your index file).
I'm not sure why your atoms would be moving
OK, further info on this. Looks like it's the minimizer, at least in
the case of freeze groups. I'm using l-bfgs; it seems the minimizer
doesn't respect the constraints imposed by freeze groups.
Now that I think of it, I seem to remember that most of the minimizers
in GROMACS don't respect constr
Bob,
Maybe this is a stupid suggestions butdid you check if your two
atoms are centered in the box and that the box dimensions are big
enough to accomodate your system? Maybe the atoms appear to be "flying
apart" because periodic boundary conditions are being applied.
They're not "flying a
Maybe this is a stupid suggestions butdid you check if your two
atoms are centered in the box and that the box dimensions are big
enough to accomodate your system? Maybe the atoms appear to be "flying
apart" because periodic boundary conditions are being applied.
Bob
On 3/16/07, David Mobley
All,
I'm trying to be ultimately able to fix the position of several
arbitrary atoms (think of them just as spheres) in a simulation. One
would think this should be straightforward, but I'm having big
problems.
In particular, right now I'm just using two atoms, which I initially
have at a separa
Mark Abraham wrote:
I think a warning is a good idea, but maybe 10 is even on the low side
for that. Since temperature is macroscopic, you'll need enough atoms
not to deviate too much from the target temperature. I have no
evidence on which I can make a proper suggestion... My bidding will be
50!
Dear ALL:
Is it documented somewhere how can one add a new non-bonded force field
into Gromacs? I'm interested on adding the Stillinger-Weber force field,
with two and three body contributions. Has anyone ever tried this
before?
Thanks in advance for your answers.
Best wishes,
Adama
Triguero, Luciano O wrote:
Dear Users,
Thank for your help. I started a 10 ns simulation, but it dies because of an error in the cluster PBS system,
so I want to continue the simulation from the last (r,v) point. May I still use
tpbconv to restart from that last point and continue the simulat
2007/3/16, andrea spitaleri <[EMAIL PROTECTED]>:
Qiao Baofu wrote:
>
> When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr].
fine. this is clear, where rho = N/V and N = number of particles (7 ions
in this case)
and V is the total Volume.
N is the total number of the atoms to
Dňa Pi 16. Marec 2007 14:19 Triguero, Luciano O napísal:
> Dear Users,
>
> Thank for your help. I started a 10 ns simulation, but it dies because of
> an error in the cluster PBS system, so I want to continue the simulation
> from the last (r,v) point. May I still use tpbconv to restart from that
>
Hi Luciano,
As mentioned, yes you can, that's what tpbconv is for (primarily); tpbconv -h.
Tsjerk
On 3/16/07, Triguero, Luciano O <[EMAIL PROTECTED]> wrote:
Dear Users,
Thank for your help. I started a 10 ns simulation, but it dies because of an
error in the cluster PBS system,
so I want to
Dear Users,
Thank for your help. I started a 10 ns simulation, but it dies because of an
error in the cluster PBS system,
so I want to continue the simulation from the last (r,v) point. May I still use
tpbconv to restart from that last point and continue the simulation.
Thank again,
Luciano
Check the manual for file format.
Following steps are for your reference
How to Create Topology from PRODRG
1. Save the topology from PRODRG (what you pasted below) into an itp
file, e.g. ptr.itp. Save the PDB section into ptr.pdb.
2. Use your text editor, enter
#include "ffG"
#include
Hi.
I want to use the ff oplsaa with tip4p water (as suggested in the manual).
Using:
genbox_d -cp hpo4_box.pdb -o hpo4_water.pdb -cs tip4p.gro
creates a good pdf-file with tip4p-water, but the following:
pdb2gmx_d -f hpo4_water.pdb -o hpo4_water.gro -p hpo4_water.top -ff oplsaa -n
hpo4_water.n
Can you be more specific? Continue or start new simulation. Use tpbconv
to extend your simulation.
On 3/16/2007 9:37 AM, Triguero, Luciano O wrote:
Dear users,
How do I restart a gromacs simulation?
Ciao,
Luciano
Dr. Luciano Triguero College of Art and Science Department of Physics and
Hi Ozge,
'sidechain' indicates all side chains present in your system, i.e.
everything designated 'protein' based on residue names, excluding
everything taken to be 'backbone' based on atom names.
You'll probably have to run the program three times to get the
combinations of minimal distances be
Hi,
I forgot to ask my other question :) When I use the g_mindist command, it asks
me to select two groups for which the distance will be calculated. I am
confused for the following: I want to calculate the minimum distance among
three side chains of my molecule in all combinations. So, if I c
Hi,
I want to calculate the number of solvent molecules within a cutoff distance
around the protein molecule. I could not find the appropriate command for this
in manual. Moreover, I could not understand the information for g_sorient.Could
you give me a more detailed explanation for this?
Than
Qiao Baofu wrote:
>
> When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr].
fine. this is clear, where rho = N/V and N = number of particles (7 ions in
this case)
and V is the total Volume.
> Therefore, the efficient volume is (10x10x10). this may give you N=6.
why the efficient
Hi,
On Friday, 16. March 2007 00:36, Michal Walczak wrote:
> Hello everyone,
>
> Can anyone tell me or post me publication or link which contains
> information how GROMOS force field differs from Amber ff.
A rather new article about popular forcefields and some statistical results
from them:
Ma
2007/3/16, [EMAIL PROTECTED] <[EMAIL PROTECTED]>:
Hi all,
I am struggling with the rdf. I have 7 structural ions in my protein and
I'd like to monitor the coordination number around them (ion - protein)
during my MD. I have read papers about it and:
http://www.gromacs.org/pipermail/gmx-users/200
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