Dear Justin,
Would you please tell me how, give me an example code, because I'm a novice?
Thanks in advance,
Marwa
On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote:
>
>
> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote:
> > Dear gmx-users mailing list team,
> > I want to know how to fix the
Hello,
you'll need to check if you are properly sampling the different states
in your simulations, which should be possible by analyzing the
histograms you can get from gmx bar -oh
Otherwise you'll need to check if your simulation parameters are
realistic, as the program warns you :)
Dear Gromacs experts,
I have generated topology files(.itp) of the ligand from the ATB server and
everything goes well, but when it comes to generating ions.tpr file, I am
getting following error.
$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
:-) GROMACS -
On 2/13/20 1:33 PM, Marwa Abd El Kader wrote:
Dear gmx-users mailing list team,
I want to know how to fix the separation of 2 chains after the production
run. I'm trying different combinations of trjconv after creating an index
file having a specific residue(s) on the interface between the 2
On 2/13/20 8:56 AM, Atila Petrosian wrote:
Hi gromacs users,
I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
water molecules) using gromacs 2019.
I used ATB for drug molecules and Tieleman's web site for lipid molecules.
ATB uses a custom version of GROMOS96 that
On 2/13/20 5:59 AM, Christian Blau wrote:
Hello Matthias,
yes, if you use an indexfile with exactly one index group inside, this
index group will be automatically picked.
(like
[ solvent ]
1001 1002 1003 1004 1005 1006 1007 1008 1009 ...
and nothing else
It's even easier than
Dear Gromacs users
I am doing free energy calculation of a ligand with protein. When I do gmx
bar it gives me the following error:-
Temperature: 298.15 K
Detailed results in kT (see help for explanation):
lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/-
0 1
Dear gmx-users mailing list team,
I want to know how to fix the separation of 2 chains after the production
run. I'm trying different combinations of trjconv after creating an index
file having a specific residue(s) on the interface between the 2 chains,
but nothing is working. I fixed this issue
You can use compel and build a double bilayer system to separate ions. However,
if you separate positive and negative ions, you will have very high membrane
potential, event two ions difference can raise potential about 200 mV. In your
case, I suppose 500 mV is not enough to separate all ions
Hi,
On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari <
ali.khoday...@student.kuleuven.be> wrote:
> Dear Gromacs users,
>
> I’ve got a question regarding the tabulated potentials for bonded
> interactions.
>
> Gromacs recognises and reads the non-bonded potential tables through the
> energy groups
Hi gromacs users,
I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
water molecules) using gromacs 2019.
I used ATB for drug molecules and Tieleman's web site for lipid molecules.
---
My topology file is as follows:
Hello Matthias,
yes, if you use an indexfile with exactly one index group inside, this index
group will be automatically picked.
(like
[ solvent ]
1001 1002 1003 1004 1005 1006 1007 1008 1009 ...
and nothing else
Best,
Christian
On 2020-02-13 11:49, Urban, Matthias wrote:
Hello
Hello mailinglist,
is there a way to prevent "gmx genion" from expecting input via stdin?
I am using gromacs v2020 with gmxapi.
Thanks in advance.
Cheers,
Matthias
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Anyone has advice/feedback?
On 06/02/2020, 16:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Luirink, R.A." wrote:
Here some output to illustrate what I mean. This is what you would expect
and what I also get for standard atom-atom interactions, not 1-4 and not
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