Hi,
Which version of Gmx are you using?
I ask because of a recent bug fix. The bug was that I tried to print the value
of an environment variable, without checking if that variable was set, causing
set faulting.
Make sure the GMX_QM_GAUSS_DIR (for Gmx < 5 GAUSS_DIR) are set and point to the
Hi,
I have a protein with four domains.
I know the conformation of the full protein in one state.
In the other state I know only the conformation of two of the domains.
I would like to move the two domains, whose positions are known in both
conformations, and observe movements in the other two
Hi,
None of this matters - you care about whether the force field was
parameterized to model a single-residue zwitterion, and papers looking and
side-chain analogues literally do not matter. Checkout the original
literature (which you should have done before choosing the force field!)
Mark
On
Hi,
Unfortunately, most of the works on single amino acides which I have seen
already focused somehow on amino acid side chains only, by truncating the
amino acid in \alpha Carbon and removing the whole backbone, then no
zwitterion issue in single amino acid comes up whatever force field are
Hi,
I don't know, but perhaps your background reading about your choice of
forcefield will prove informative about what has or has not been
parametrized or tested ;-)
Mark
On Sat, Jun 11, 2016 at 8:37 PM Alexander Alexander <
alexanderwie...@gmail.com> wrote:
> Hi,
>
> Yes, I am going to
Hi,
Yes, I am going to calculate the free energy of single amino acid (in their
zwitterion form) in water.
I did not get your point, you mean that neither of them can not be used for
zwitterion form if the system is a single amino acid in water? Then how a
single amino acid (in zwitterion form)
Hi,
The zwitterion form modifies the alpha carbon charge, so can't be used
together for a single amino acid in this case. We should add a check that
stops you running into this problem. It wasn't clear in your first post
that you were trying to get a topology for a single amino acid.
Mark
On
Thanks for your response Mark.
To keep the zwitterions form, two below possibilities are offered for
terminies:
0: NH3+
1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
With "0:" the "-0.110 e" charge shows up while with "1:" it goes fine, but
what the differences
Hi,
Look at your topology and consider where the charges go wrong. Probably
your termini selections are inappropriate.
Mark
On Sat, Jun 11, 2016 at 7:11 PM Alexander Alexander <
alexanderwie...@gmail.com> wrote:
> Dear gromacs user,
>
> I am expecting to get a uncharged GRO file of the
Dear gromacs user,
I am expecting to get a uncharged GRO file of the Glutamic acid by invoking
below command, and selecting the protonated version of it, but I do not
know why I get unexpected total charge of "-0.110 e" at the end when I use
the OPLS-AA force field while the other FF's result to
Uliano,
Thanks for the update! Such info is always useful to share.
Weird indeed and as I have not much OS X experience I can't comment on
most of this stuff -- except one bash-ism that may help rendering your
shell useless after setting the dynamic library path.
[env] MY_ENV_VAR=value gmx
Dear Gromacs users
I have a question about the concept of the compressibility factor in
.mdp
file. suppose I assign Compressibility in X direction equal to zero. does
this mean that the atoms in X direction cannot move at all or just the
size of the� simulation box� in this
HI all, I’m resuming this thread with some updates
I “believed" to have set them, however for (silly?) security reason since OSX
10.11 with the introduction of System Integrity Protection (SIP) Apple
disallows the user to see the content od environment variables starting with
DYLD* and to
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