Thanks for reply. Yes, it uses the force-field file I created.
Basically I found out that the dihedral which the program skips is
also 0.
On Apr 12, 2007, at 8:43 PM, Dallas B. Warren wrote:
Can't really help you directly, but it comes to mind when I read that
error that may be something is
Can't really help you directly, but it comes to mind when I read that
error that may be something is incorrectly defined or formatted within
your files. It is not picking up the actual values, or something like
that? Is it using the forcefield files you created?
Catch ya,
Dr. Dallas Warren
Lect
Jagannath Mondal wrote:
Hi David,
Thanks for your email. But then what is the purpose of
option like gb_algorithm, nstgbradii =1 etc.
Is there any way I can do implicit solvent simulation using any
other interface?
Try AMBER.
Mark
___
Hi David,
Thanks for your email. But then what is the purpose of
option like gb_algorithm, nstgbradii =1 etc.
Is there any way I can do implicit solvent simulation using any
other interface?
Thanks,
Jagannath
On Apr 12, 2007, at 5:06 PM, David van der Spoel wrote:
Jagan
Jagannath Mondal wrote:
Hi,
I am trying to learn how to use implicit solvent model for PMF
calculation. For that ,I wanted to know what are the options for
implicit solvent present in gromacs. But I could not find any
documentation regarding that. I searched mailing list and found that
Hi,
I am trying to learn how to use implicit solvent model for PMF
calculation. For that ,I wanted to know what are the options for
implicit solvent present in gromacs. But I could not find any
documentation regarding that. I searched mailing list and found that
there has been some q
Thanks a lot, Berk. This is exactly the answer I was hoping for,
meaning it's clear for me now.
Jeroen
> Date: Thu, 12 Apr 2007 13:42:42 +0200
> From: "Berk Hess" <[EMAIL PROTECTED]>
> Subject: RE: [gmx-users] soft-core potential in combination with PME
> (sorry, again)
> To: [EMAIL PROTE
pkmukher wrote:
Dr Spoel,
Thanks for your suggestions. Actually i would be using the
GROMOS96 force field(option 0 in pdb2gmx GROMOS96 43a1).I am
new to the GROMACS package.I wish to simulate a
ligand-protein system and had been using the drug-enzyme
tutorial available for this purpose. In the
Hi,
I am trying to prepare a gromacs topology file for a non-natural
peptide. For that I prepared a molecule.itp file and a corresponding
ff***bon.itp file which contains all the bond-type, angle-type and
dihedral-type.
But, when I try to use
grompp for generating the .tpr file, it sho
Dr Spoel,
Thanks for your suggestions. Actually i would be using the
GROMOS96 force field(option 0 in pdb2gmx GROMOS96 43a1).I am
new to the GROMACS package.I wish to simulate a
ligand-protein system and had been using the drug-enzyme
tutorial available for this purpose. In the tutorial they
use
Joern Lenz wrote:
i know what this error message means. Their 1-4 distance is too long.
Their 1-4 distance *becomes* too long. It is likely this is because
of a topology problem that has nothing directly to do with the 1-4
interactions. Check the relevant region carefully.
the menti
dear gromacs guys,
i have the following problem:
i linked the phosphate atom of a DNA to the phenolic-hydroxyl group of a
proteins tyrosine by defining a line in the specbond.dat file.
the distance before linking these atoms was about 4.2 angstroms.
my intention now was first to minimize the link
sorry, but i forgot to say that the distance between this tyrosine and the P
of the DNA was from a previously calculated MD simulation.
when i tried to add the following line into the (see below) mdp file:
table-extension = 2
the warning messages becomes
Warning: 1-4 interaction between 8159 and
Hi,
Thank you for your response. I have another question regarding the
implementation of replica exchange in Gromacs. In order to run such a
simulation on version 3.3 I need to install the LAM/MPI version of Gromacs
and load the appropriate modules on the cluster (at the moment we use
scor
Dear GROMACS User,
I would like to perform a MD simulation (using a united-atom force field) of a
receptor in a lipid bilayer, introducing a ligand which contains covalently
bound flour.
The problem is:
(1) The GROMOS-96 force field only deals with single non-ionic flour atoms and
not with th
I don't know about Anwars paper.
But I can say that their is no fundamental difference between PME
and RF with soft-core. With the GROMACS setup they converge
to exactly the same energies at any lambda value when you increase the RF
cut-off.
I don't understand what David Mobley meant exactly.
T
Hi Berk (and others),
Thanks a lot for your quick answer. And sorry to bother you again
with this long email, but I still feel I'm missing something really
essential here.
I agree that in essence the convergence and the singularity are two
different problems. And if I understand you correctly,
From: Manuel Valera <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: [gmx-users] wall_atomtype
Date: Wed, 11 Apr 2007 18:53:15 -0700 (PDT)
Greetings to All
I have a question about a new feature in the cvs code
and I was wonder
Soft-core interactions are fully supported with PME.
Both mails you quote do not state otherwise.
The second mail refers to convergence issues when
switching off LJ as well as electrostatics interactions.
This problem will (probably) always be present, and has
nothing to do with the singularities
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