On 11/19/18 8:52 PM, Kovalskyy, Dmytro wrote:
Justn,
Then there are force fields that do better than others, but
the choice must be yours based on a thorough review of available
literature;
Can you provide a list of FFs more suitable for folding and IDP simulations?
This is a complicated
On 11/20/18 12:02 PM, Lakshman Ji Verma wrote:
Thanks, Justin,
Is there any tool in Gromacs which can give the average box angles?
g_energy only give dimensions in terms matrix parameters but not in terms
of box angles.
Maybe gmx traj -ob?
-Justin
--
==
On 11/20/18 4:48 PM, Matthew Fisher wrote:
Dear all,
I wonder if anyone could offer some advice on a current issue I've got. I'm
currently trying to simulate a Heme protein using GROMACS and the
AMBER99SB-ildn force field. Parametisation for this system has been done
previously for AMBER
Dear all,
I wonder if anyone could offer some advice on a current issue I've got. I'm
currently trying to simulate a Heme protein using GROMACS and the
AMBER99SB-ildn force field. Parametisation for this system has been done
previously for AMBER (
https://doi.org/10.1002/jcc.21922
) and throu
Thanks, Justin,
Is there any tool in Gromacs which can give the average box angles?
g_energy only give dimensions in terms matrix parameters but not in terms
of box angles.
Thanks
Lakshman
On Mon, Nov 19, 2018 at 5:53 PM Justin Lemkul wrote:
>
>
> On 11/19/18 5:42 PM, Lakshman Ji Verma wrote:
>
Hi,
gromacs started dying on me lately with rather obscure error messages as in the
caption of this mail. Errors seem to be related to the nvidia driver (see below
for more output,and further below for the mdp file) ... i perform a large
number of short (2ns) sims and this happens perhapsone ou
Hi,
Please try to use a descriptive subject for your email... you'll have a
better chance of getting the help you actually want ;-)
On Tue, Nov 20, 2018 at 3:40 PM Emmanuel Broni
wrote:
> Hello Gromax Users,
> I was running a 100ns MD simulation on an hpc and it was terminated with
> the follow
Hello Gromax Users,
I was running a 100ns MD simulation on an hpc and it was terminated with
the following comments in the log file. What does it mean and what do I do?
DD step 39 load imb.: force 17.8% pme mesh/force 0.925
step 120 Turning on dynamic load balancing, because the performance lo
Hi,
On Tue, Nov 20, 2018 at 2:45 PM John Whittaker <
johnwhitt...@zedat.fu-berlin.de> wrote:
> Hi Justin, thanks for the reply and the good idea.
>
> I checked a configuration of my system using both force fields and, for
> the information of anyone who may have a similar problem in the future,
>
Hi Justin, thanks for the reply and the good idea.
I checked a configuration of my system using both force fields and, for
the information of anyone who may have a similar problem in the future,
found using gmx energy:
CHARMM36 from Tom Piggot on GROMACS website:
Energy Aver
Hi,
the most likely issue is that your GROMACS installation is not configured
for the correct architecture; e.g. if the compute or login node that the
cmake configure/compilation was done on is newer than the one that's
running on, mdrun will try to issue instructions that are not supported by
the
On Tue, Nov 20, 2018 at 7:12 AM Seketoulie Keretsu
wrote:
> Dear Benson,
>
> Thank you for answering .
> I am using Centos 6. My current simulation time for protein-ligand
> systems is about 1.6 ns/day. I am wondering if installing the GTX 1050
> or GTX 970 can boost the output significantly (may
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