On 6/26/13 8:39 PM, Neha wrote:
Hi everybody,
My runs keep crashing despite energy minimisation and fiddling around with
nstlist values. I have been looking in the Gromacs manual particularly the
interaction ranges in the domain decomposition section, which mentions that
simulations can stop w
Hi everybody,
My runs keep crashing despite energy minimisation and fiddling around with
nstlist values. I have been looking in the Gromacs manual particularly the
interaction ranges in the domain decomposition section, which mentions that
simulations can stop with error messages about missing int
Justin Lemkul wrote
>>
>
> What was the outcome of EM before this? What if you try NVT before NPT?
> Have
> you tried reducing the timestep or the value of nstlist?
>
> I would try everything with ref_p = 1.0 instead of zero to make sure you
> can get
> a "normal" setup to work.
>
> -Justin
Addendum:
On 19.06.2013 23:16, Mirco Wahab wrote:
...
MARTINI W is a strongly associating fluid and will freeze
trough your box in no time even when setting negative pressure
below 300K. In newer Gromacs versions (from 4.6) there seems
to be additional shift (?) in the potential, so the water ph
On 19.06.2013 15:25, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
dt = 0.02
Should be 0.03 according to S. Marrinks own remarks
(but wouldn't change your experience)
nstcomm
On 6/19/13 9:25 AM, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit= 0.0
dt = 0
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit= 0.0
dt = 0.02
nsteps = 5
On 6/18/13 10:12 PM, Neha wrote:
Hi,
Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.
Please post a full .mdp file; parti
Hi,
Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.
Justin Lemkul wrote
> On 6/18/13 3:13 PM, Neha wrote:
>> Hi everybody!
>>
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