Hello gromacs users,
I just modified opls force field for a modified aminoacid with 4 new bond types
and 9 new angle types. However, the command grompp gave a no default error for
one bond and 6 angle types. Is there a way to resolve this?
Many thanks and Take care,
Neena
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Gromacs Users
hi allI want to download a topology of co2 by opls as forcefield, but many
servers doesn't answer(like ligpargen and tppmktop). how can I find a topology
for this molecule?
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Gromacs Users mailing list
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Hi everyone,
I'll be straight, my questions are:
1. It is possible to use Drude model in GROMACS 5.1.5?
2. How exactly this is done? If someone had an input file example (pdb
and/or itp) and can share it i'll appreciate.
Thank a lot!!
Nicolas Rozas Castro
Universidad de Chile
--
Gromacs Users
Hi,
There could certainly be a bug with -ddorder pp_pme, as there's no testing
done of that. If you can reproduce with a recent version of GROMACS, please
do file a bug report. (Though this week we're moving to new infrastructure,
so leave it for a day or two before trying to report it!
Mark
On
Hi,
> Am 24.03.2020 um 16:28 schrieb Tobias Klöffel :
>
> Dear all,
> I am very new to Gromacs so maybe some of my problems are very easy to fix:)
> Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the
> benchmarks are taken from:
>
On 3/24/20 3:26 PM, Daniel Bauer wrote:
Hi,
I am trying to convert forcefield parameters of zwitterionic glycine
from an amber object file format to gromacs .rtp (to use it with
amber99sb, which lacks zwitterionic amino acids).
The amber library file I plan to use can be found here:
Hi,
I am trying to convert forcefield parameters of zwitterionic glycine
from an amber object file format to gromacs .rtp (to use it with
amber99sb, which lacks zwitterionic amino acids).
The amber library file I plan to use can be found here:
Hello gmx users!
I just finished the transition of our project database to use the Gitlab
servers.
This means that from now on issues should be reported using the issue
tracker at https://gitlab.com/gromacs/gromacs/-/issues instead of
redmine.gromacs.org.
The redmine and gerrit servers have
Dear all,
I am very new to Gromacs so maybe some of my problems are very easy to fix:)
Currently I am trying to compile and benchmark gromacs on AMD rome cpus,
the benchmarks are taken from:
https://www.mpibpc.mpg.de/grubmueller/bench
1) OpenMP parallelization: Is it done via OpenMP tasks? If
Dear Gromacs users
I ran an MD simulation for 3ns and from the last coordinates started a free
energy calculation for 3ns. My system is well equilibrated but after 710725
steps I am getting Lincs warning every time as below:-
WARNING: There are no atom pairs for dispersion correction
starting
On 3/24/20 3:09 AM, Wesley Michaels wrote:
Hi,
Thanks for your reply! I built the topology with my own script, as opposed
to using pdb2gmx. Following Bogdan's instructions here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html),
I specified all
Hi,
Sorry to bother you. Recently, I have encountered a problem when running free
energy calculation of a dna-ligand complex system. The structure start to
getting weird when I try to specify the two state (A,B) in the topology file,
which is never spotted in the unconstrained MD simulations.
Hi,
Thanks for your reply! I built the topology with my own script, as opposed
to using pdb2gmx. Following Bogdan's instructions here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html),
I specified all instances of 1-4 pair interactions (i.e. pairs of atom
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