Dear Chris
Thank you very much for giving your comprehensive information on my mdp
options.
In my current simulation, I am trying to switch off coulombic interactions
while keeping VDW on.
In gromacs manual, it is mentioned that with parallel simulations and/or
non-bonded force calculation on the
Hello,
sorry for the confusion, but I'm currently moving our infrastructure
over to Gitlab and have set Redmine to read only because of this.
I'll update gmx-users and gmx-developers once the process is done, and
then you can open the issue on Gitlab using the tracking system there.
Cheers
Hi Magnus and Justin,
Am 23.03.20 um 13:52 schrieb Magnus Lundborg:
> Hi Jochen,
>
> Have you tested if this happens with -update cpu? Perhaps it's the
bonded on GPU that's the problem, unrelated to updating.
The problem only appears with -update gpu, not with -update cpu.
I didn't see a
>
Thanks, Justin!
On 23.03.20 17:34, Justin Lemkul wrote:
On 3/23/20 12:30 PM, Daniel Burns wrote:
Hi Johannes,
Somebody please correct me if I'm wrong but I believe it is just the
thermostats that are exchanged.
There's a lot of information that is exchanged, including temperature
and
On 3/23/20 12:30 PM, Daniel Burns wrote:
Hi Johannes,
Somebody please correct me if I'm wrong but I believe it is just the
thermostats that are exchanged.
There's a lot of information that is exchanged, including temperature
and pressure coupling information, coordinates, velocities, and
Hi Johannes,
Somebody please correct me if I'm wrong but I believe it is just the
thermostats that are exchanged.
A given simulation box's velocities are rescaled accordingly after the
exchange and the simulation continues with its own fluctuations in box size
assuming it is pressure-coupled.
I
Dear all,
I have slightly different Position Restrains and Box sizes over my
lambda windows in an alchemical Free Energy Calculation in NVT ensemble
(I know that my calculated Free Energy Difference will not solely depend
on the mutation alone..)
What happens if I use replica exchange? What
Hi Magnus,
Thanks for the response.
As I said before the system contains the "thin film + molecule A ( single
molecule) intended for the PMF calculation + Water".
And actually by the “comm-grps = thin film” the gmx grompp failed as some
atoms are not part of any center of mass motion removal
Hi Alex,
Using
"comm-grps = thin film"
should be right, yes. In theory
"comm-mode = Linear-acceleration-correction"
could improve things, but is mainly useful if you are actively pulling
the molecule through, i.e., what you are probably doing when generating
the windows.
There was a user
Hi Jochen,
Have you tested if this happens with -update cpu? Perhaps it's the
bonded on GPU that's the problem, unrelated to updating. I didn't see a
Redmine issue yet. Could you make one?
Cheers,
Magnus
On 2020-03-19 18:01, Jochen Hub wrote:
Hi developers,
I am running a simple DPPC
Hi
I have a 1000ns simulation of gpcr protein. The protein structure have 7
helix.
1. How will I calculate the tilt of each helix?
2. If it has to be done by generating the index file, what groups are meant
to be added for index file?
3. What groups should be chosen when gmx bundle prompt to
Hi
On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels
wrote:
> Hello,
>
> I hope this message finds you well! I'm running a pretty simple simulation
> of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P =
> 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are
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