Dear gromacs users,
I was trying a simple gmx solvate test on a water box of size 25*20*20
angstrom, creating a water box of density 1 g/cm^3. By my calculations
the no. of water molecules in the box should by 332 (each water molecule
has a volume of (3.11 angstrom)^3). When I use the solvate
Hi,
I have been a new user and i was following the protein-ligand complex
tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology
i have used ATB webserver. I did download the .itp and .pdb file from there
and converted that to .gro file. The problem i am facing is it shows an
Dear Kushal,
Regarding the first error, I feel that you have done a few mistakes while
updating your topology section as your system has more atoms than what is
in the topology. Kindly go through the tutorials on this site -
http://www.mdtutorials.com/gmx/index.html, to get a picture on how to do
Hello,
if you have found a bug in the multi-dimensional array please report it
on redmine.gromacs.org so we can fix it, together with the build
configuration that causes it.
Cheers
Paul
On 14/03/2020 00:51, Alexander Tzanov wrote:
The new version from March 2020.1 is buggy. Try version
Hello everyone
I am looking for a sample Gromacs script and a Plumed file with Distance
Colvar. Please send me one if feasible.
--
Cheers
Peter
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't
I generate a box of 100 molecules of methyldiethanolamine with insert-molecules
command .I downloaded its itp file from ATB server. I think that forcefield is
gromos . after an energy minimization the potential energy is positive. the
mdp file is attached.
Sent from Yahoo Mail on Android--
Hi Billy,
1. Firstly, why is that gromacs reads MYR as residue 2 and not 1? What does
it say in your PDB file?
2. There is no atom labelled C in your MYR atom list. Looks like you have
listed atom C in the dihedral type (ffnonbonded.itp), change that.
3. If you think it is not
On 3/14/20 7:15 PM, Afsane Farhadi wrote:
I generate a box of 100 molecules of methyldiethanolamine with insert-molecules
command .I downloaded its itp file from ATB server. I think that forcefield is
gromos . after an energy minimization the potential energy is positive. the
mdp file is
On 3/14/20 8:05 PM, Afsane Farhadi wrote:
what do I have to do for solving this mater? I want to use a opls as
forcefield. how can I find that forcefield for methyldiethanolamine?
http://zarbi.chem.yale.edu/ligpargen/
-Justin
Sent from Yahoo Mail on Android
On Sun, Mar 15, 2020 at
On 3/14/20 1:59 AM, Billy Williams-Noonan wrote:
Hi Experts,
This is a long-ish e-mail so thank you very much for your time
I am using the GROMACS compatible charmm36 forcefield for
betapeptides described here:
https://gitlab.com/awacha/charmm-beta.ff
In merged.rtp I have redefined the MYR
what do I have to do for solving this mater? I want to use a opls as
forcefield. how can I find that forcefield for methyldiethanolamine?
Sent from Yahoo Mail on Android
On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote:
On 3/14/20 7:15 PM, Afsane Farhadi wrote:
> I generate a box of
thank you so much Mr.justin
Sent from Yahoo Mail on Android
On Sun, Mar 15, 2020 at 3:38, Justin Lemkul wrote:
On 3/14/20 8:05 PM, Afsane Farhadi wrote:
> what do I have to do for solving this mater? I want to use a opls as
> forcefield. how can I find that forcefield for
Hi Experts,
This is a long-ish e-mail so thank you very much for your time
I am using the GROMACS compatible charmm36 forcefield for
betapeptides described here:
https://gitlab.com/awacha/charmm-beta.ff
In merged.rtp I have redefined the MYR residue hoping I could link it to
the N-terminus of
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru
Vincent
14 matches
Mail list logo
