Good morning!
I would like to use one of the MM force fields (originally by Allinger) in
GROMACS. Has anyone tried to adapt such a force field?
I know of at least two previous inquiries:
Corina Barbu in 2003: http://www.gromacs.org/pipermail/gmx-users/2003-October
Konrad Piwowarczyk in
Inon Sharony wrote:
Good morning!
I would like to use one of the MM force fields (originally by Allinger)
in GROMACS. Has anyone tried to adapt such a force field?
Short answer: No.
It should not be too hard if you want to try (that is if the functional
form is implemented already).
Hi,
Position restraints do not allow me to do what I want.
For instance, I want to allow the system to freely explore the conformational
space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff.
Another application would be to push the system conformation away from the
Sam Moors wrote:
Hi,
Position restraints do not allow me to do what I want.
For instance, I want to allow the system to freely explore the
conformational space within a certain RMSD range, but not evolve beyond
a specified RMSD cutoff.
Another application would be to push the system
Another possibility is to patch gromacs with PLUMED
http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
Here RMSD (and derivatives) is already implemented and you can
easily restraint your MD simulation within a certain RMSD cutoff
from a reference structure.
Massimiliano
On May 19, 2009, at
Hi,
You can also use essential dynamics sampling.
Ran.
David van der Spoel wrote:
Sam Moors wrote:
Hi,
Position restraints do not allow me to do what I want.
For instance, I want to allow the system to freely explore the
conformational space within a certain RMSD range, but not evolve
Hi all
I am looking for a way to import forces from a gromacs run into VMD for
analysis. From a mdrun rerun I have forces in a .trr file but VMD only
reads the coordinates. Can you think of any way to get the forces into vmd
instead of the coordinates?
Thank you!
Matteus
Hi David,
Thanks for your suggestion.
However, I have a problem with the use of distance restraints in gromacs. As
described in the manual a restraint potential is applied to each pair of atoms
separately. Instead, I would like the restraint potential to depend on the
root mean square of pair
Hi,
Sorry to pull a self-publicity plug, but you could use our MDDriver
library [1] to implement whatever constraint you want as long as it
can be calculated from the system positions and translates into
forces to be applied to your system.
Such a 'scripting' application is very briefly hinted
Hello,
I have a DNA-Zinc finger complex. What are the suitable forcefields
for that type of complexes (the zinc ion is coordinated to 4
deprotonated cysteines)?
I need to do some molecular minimization and dynamics including the
nucelic acid sequence.
Looking for some help.
Thank you.
Dear all
I want remove water molecules from hydrophobic core of
lipid by using script Keepbyz.pl by (chris neale) . I want to know basis
of deciding uprez and lowrez variables . I mean to say how can I decide
which value of uprez and lowrez is suitable for my system protein
nitu sharma wrote:
Dear all
I want remove water molecules from hydrophobic core of
lipid by using script Keepbyz.pl by (chris neale) . I want to know
basis of deciding uprez and lowrez variables . I mean to say how can I
decide which value of uprez and lowrez is
Nehme El Hachem wrote:
Hello,
I have a DNA-Zinc finger complex. What are the suitable forcefields for
that type of complexes (the zinc ion is coordinated to 4 deprotonated
cysteines)?
The first step is probably to search in the literature for anything similar.
Has anyone attempted such
Hi,
Have a look at
http://wiki.gromacs.org/index.php/Parameterization
and
http://wiki.gromacs.org/index.php/Exotic_Species
Next to that, also consider that you are talking about a site with -2
formal charge (ZnS4)2-. How likely is that? From QM studies, it seems
much more likely that there are
Dear all,
I want to study glycolipid-protein interaction using united atom
GROMACS force field.
For lipid simulation we need lipid.itp, which is a mixture of lipid (
Berger) and GROMOS (ffgmxnb) parameters.
Matteus Lindgren wrote:
Hi all
I am looking for a way to import forces from a gromacs run into VMD for
analysis. From a mdrun –rerun I have forces in a .trr file but VMD only
reads the coordinates. Can you think of any way to get the forces into
vmd instead of the coordinates?
If VMD
Dear gmx-users,
I have done a test using test suit 4.0.4, and I got some failures as follows.
All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
4 out of 14 complex tests FAILED
FAILED. Check files
Bert wrote:
Dear gmx-users,
I have done a test using test suit 4.0.4, and I got some failures as follows.
All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
4 out of 14 complex tests FAILED
Hi,
g_traj can write |f| or components of f in the b-factor field of a pdb file.
I guess VMD can read and display that.
I don't know if that will fulfill your needs.
Berk
Date: Wed, 20 May 2009 00:19:59 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users]
Hi all users,
I am wondering how I can apply the shear force into the gromacs .Does anyone
has such experoence about that?
Really appreciate any suggestions.
Yang
___
gmx-users mailing listgmx-users@gromacs.org
Hi,
Read the pdf manual, it has an index entry for shear.
Berk
From: yang...@mavs.uta.edu
To: gmx-users@gromacs.org
Date: Tue, 19 May 2009 15:10:24 +
Subject: [gmx-users] how to apply shear force
Hi all users,
I am wondering how I can apply the shear force into the gromacs .Does
Dear GMX-users.
I'm trying to do free energy calculations for calculations of
partitions coefficients.
My normal defaults section of TraPPE topologies are:
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 no
0.5 0.5
because TraPPE don't use 1-4 LJ interaction, and I have
sovent accesible surface area?
On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
stretching != swelling, e.g.
On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote:
How about checking radius of gyration???
2009/5/18 Tsjerk Wassenaar tsje...@gmail.com
Hi All,
Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
yes, I will be appreciated if he/she can tell me how to run gmx on this
facility. I either get error messages which says either the executable or
the topology file can not be found.
Regards,
Payman
Well, why didn't I think of that? Maybe because flattening will also
increase the SAS, or (partial) unfolding, or opening of two domains...
:)
Tsjerk
On Tue, May 19, 2009 at 6:10 PM, Marius Retegan
marius.s.rete...@gmail.com wrote:
sovent accesible surface area?
On Mon, May 18, 2009 at 11:09
Dear David:
Thank you so much for the valuable information.
Our conclusion in the above paper is to use PME for Coulomb and not shift
Van der Waals
I have read the paper you mentioned and did not find how you treated the
VdW. Have you done some work on the cut off method for vdw? Since I used
Sam Moors wrote:
Hi David,
Thanks for your suggestion.
However, I have a problem with the use of distance restraints in
gromacs. As described in the manual a restraint potential is applied to
each pair of atoms
separately. Instead, I would like the restraint potential to depend on the
root
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give more information regarding
the output. Then
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming that
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a
Payman Pirzadeh wrote:
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming that
Dear all:
This is the mdp I just used for the system. The funny thing is after a 8ns
simulation I got a very high pressure and temperature:
Temperature 343.437
Pressure (bar) 45.782
I also did another run with removing the vdw_switch in mdp and keep all
other
Hi Justin,
Following is the script I use. But remember several points:
1. I compiled the gmx with double precision and did not rename the code to
mpi. I kept whatever was produced with _d suffix.
2. I use the same script for other codes and they work (I am using other MD
code for special purposes
Payman Pirzadeh wrote:
Hi Justin,
Following is the script I use. But remember several points:
1. I compiled the gmx with double precision and did not rename the code to
mpi. I kept whatever was produced with _d suffix.
Whatever was produced does not inspire confidence. You're sure that
Hi
I want to get the simulation results fater and want to set
the time step
dt = 0.002
what is the upper limit of the time step dt ?
Thank you
Lin
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gmx-users mailing listgmx-users@gromacs.org
Chih-Ying Lin wrote:
Hi
I want to get the simulation results fater and want to set
the time step
dt = 0.002
what is the upper limit of the time step dt ?
Some textbook reading is probably in order here. Also of interest are papers
describing constraint algorithms. Ultimately the
Hi Lin,
I would suggest taking a look at the manual, specifically section 6.5
(Removing Fastest Degrees of Freedom), and any general textbook on
molecular simulation. Wanting faster results without having an
understanding of the method is a good recipe for getting the wrong
answer. There
I am planning on using g_clustsize to do some condensation analysis. I looked
at g_cluster and see that it has a number of method options including single
linkage and jarvis patrick. Is it true that g_clustsize has only the single
linkage option? I took a look at the source code but this type
Yanmei Song wrote:
Dear all:
This is the mdp I just used for the system. The funny thing is after a
8ns simulation I got a very high pressure and temperature:
Temperature 343.437
Pressure (bar) 45.782
I also did another run with removing the vdw_switch in
Is there a local pressure version of Gromacs 4? I can only find Gromacs
version 3.02 with local pressure. If there is, could you tell me where to get
it? Thanks.
Daniel
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf
Jacob Spooner wrote:
I am planning on using g_clustsize to do some condensation analysis. I looked
at g_cluster and see that it has a number of method options including single
linkage and jarvis patrick. Is it true that g_clustsize has only the single
linkage option? I took a look at the
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