On 6/26/18 12:42 PM, Владимир Богданов wrote:
Hey everyone!
Could you help me please?
When I make md.tpr file I get this note:
gmx_mpi grompp -f md.mdp -c npt.gro -r npt.gro -n index.ndx -t npt.cpt
-p topol.top -o md.tpr
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing
Justin,
In a previous thread on core/shell optimization (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-August/091101.html)
you state:
"No, I've made wholesale changes to the code in the way that energies and
forces
are computed. The current code has bugs. If you want a
On 6/26/18 10:37 AM, Eric Smoll wrote:
Justin,
In a previous thread on core/shell optimization (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-August/091101.html)
you state:
"No, I've made wholesale changes to the code in the way that energies and
forces
are computed.
Hey everyone! Could you help me please? When I make md.tpr file I get this note: gmx_mpi grompp -f md.mdp -c npt.gro -r npt.gro -n index.ndx -t npt.cpt -p topol.top -o md.tpr Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'Replacing old mdp entry 'xtc_grps' by
hi,
i have two protein in a system.i have already calculate the no of
contacts between two proteins.
now i want to caculate the name of the residues which are in the
contact within 5 angstrom of the two protein.
i.e the name of residues of protein1 which are in the contact with the
residue name of
So I take it then (and to confirm this) that it is an issue with the output
from gmx bar to the histogram file, rather than results from the lambda
state simulations? But the results it has presented in the results table
and final value for the free energy change is "correct"?
Previously I'd only
On 6/25/18 10:34 PM, Dallas Warren wrote:
I am trying to identify where an issue is with my free energy
calculations of an octanol molecule in octanol (and whether it is
actually an issue or not).
The lambda states used are in 0.1 increments from 0 to 1, with coulomb
interactions turned off
Hi,
gmx bar got a last-minute rewrite before GROMACS 4.6 (some implementations
of some of the free-energy algorithms changed) and I'm sure it's still in
need of love. However, the core team can't do all the things we'd like to
do, so if there are people who want to have working alternative
where i have calculate the no of contact analysis by this commands
gmx mindist -f md.xtc -s eq.gro -n index.ndx -dt 1000 -d 0.5 -on
numcount.xvg -od mindist.xvg
On 6/26/18, SHAHEE ISLAM wrote:
> hi,
> i have two protein in a system.i have already calculate the no of
> contacts between two
Dear All,
I have a question regarding the make_edi tool. I used it some time back to
restrain my structures to a particular projection value of an eigen vector
with the -restrain keyword. However, I seem to have forgotten how to set
the value of the projection in the .edi file. Does anyone here
Hi Shreyas,
> On 26. Jun 2018, at 15:21, Shreyas Kaptan wrote:
>
> Dear All,
>
> I have a question regarding the make_edi tool. I used it some time back to
> restrain my structures to a particular projection value of an eigen vector
> with the -restrain keyword. However, I seem to have
Thanks a lot, Carsten!!! Exactly what I needed :).
Shreyas
On Tue, Jun 26, 2018 at 3:41 PM Kutzner, Carsten wrote:
> Hi Shreyas,
>
> > On 26. Jun 2018, at 15:21, Shreyas Kaptan
> wrote:
> >
> > Dear All,
> >
> > I have a question regarding the make_edi tool. I used it some time back
> to
> >
Den 2018-06-26 kl. 04:34, skrev Dallas Warren:
I am trying to identify where an issue is with my free energy
calculations of an octanol molecule in octanol (and whether it is
actually an issue or not).
The lambda states used are in 0.1 increments from 0 to 1, with coulomb
interactions turned
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