Hi,
I just encountered (another) strange thing with genion.
I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp:
2, forcefield amber99sb), so I expected half of the system charge (-52)
to be added as ions. BUT it added the same amount, i.e. 52 Mg ions
instead of 26 which wou
The problem could be gen_vel=no if you are not loading velocities that are
consistent with your production temperature of 200 K. If, for example, you do
not load any velocities at all, then the initial forces will quickly be scaled
up to reach 200 K and this can cause large scale deformations/r
blems. Could you provide your mdp-file
for us to look at?
Best,
Erik
6 sep 2012 kl. 00.31 skrev Matthias Ernst:
Hi Chris,
thank you for your answer.
Let me comment on some of your hints.
refcoord_scaling is only required when you are also using positions restraints.
Therefore we need to know
be more likely? And which types of artifacts
can be caused by lack of refcoord_scaling and can they be seen or
detected easily?
Thank you very much for your help,
Matthias Ernst
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rd_scaling and can they be seen or
detected easily?
Thank you very much for your help,
Matthias Ernst
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I dont get any output and the issued command terminates in the terminal.
Do I have to remove the -o -c -g -e -x flags from the command line?
Appreciate your help,
On 13 August 2012 15:28, Matthias Ernst wrote:
Long story short: backup everything (since it's a backup, and hopefully you
won
Long story short: backup everything (since it's a backup, and hopefully
you won't need it), then use the [whatever].cpt file. You don't want to
do work twice, do you? If you use the [whatever]_prev.cpi file, you will
calculate some frames *again* that are already there.
If you use an up-to-date
Why do you want to use Gromacs?
I would suggest to use openBabel, which can convert a whole bunch of
file formats...
Regards,
Matthias
Am 10.06.2012 16:55, schrieb Lara Bunte:
Hi
Is it possible to convert a .pdb file to a .xyz file with GROMACS?
At this point there shouldn't be a force fie
utral system (with -c 0.001,
it will add 53 NA and 1 CL ions, meaning resulting salt concentration is
> 0). I use the amber99sb forcefield.
Is this behaviour desired and do I miss the point of the -neutral option
not working without specifying a concentration?
Thanks for your help,
Matthi
Hi,
I have a question regarding simulation of a protein-DNA-complex where
the protein encloses the DNA double helix. I did not find a tutorial for
a system of three rather big molecules like these, that's why I ask. If
there is such, I would appreciate a hint.
I want to start with a crystal
It is possible but not yet included in Gromacs. As far as I know, there
are several people working on porting this forcefield to Gromacs (I have
been searching for this myself last year).
Check the archives for parmbsc0 and Gromacs and search for papers that
include these terms. then you will fi
Hi,
I am currently working with the AMBER forcefields provided by GROMACS. I
noticed there are atoms in the forcefields (e.g. amber99 or amber03)
with LJ parameters of 0.0 for sigma and epsilon. For example, the HO
atom type is sometimes used (e.g. in SER or in the terminal Hs of DNA
residues
p and comments.
Best regards,
Matthias Ernst
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u answer tells me that this is impossible, so I have to change
my system.
That's not really what I expected (in fact, from a programmer's view, I
think it should be no problem to leave out terminus search) but thanks
for your help.
Matthias Ernst
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Hi,
I try to simulate DNA or better parts of a long DNA double-helix.
Therefore, the system I use is not "correctly" terminated at the ends
from chemical point of view with OH-groups but rather cut out the longer
helix. Nevertheless, all residues are named correctly, all atoms needed
in the r
olvent, boundary conditions and without cutoffs in Gromacs?
Thanks and best regards,
Matthias
Am Montag, den 12.09.2011, 14:37 +0200 schrieb Justin A. Lemkul:
>
> Matthias Ernst wrote:
> > Dear Gromacs users,
> >
> > I am currently working on porting forcefields fro
ferent,
especially the sign of the LJ term and the order of magnitude of the
Coulomb term. Why is that? What does the "SR" in LJ and Coulomb in the
Gromacs output mean?
Any help would be thankfully apreciated.
Best regards,
Matthias Ernst
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