Thanks Justin.
The help has been much appreciated.
Cheers,
Davide
On 7/02/13 8:46 PM, "Justin Lemkul" wrote:
>
>
>On 2/7/13 2:29 PM, Davide Mercadante wrote:
>> Thank you Justin,
>>
>> I guess this means that this kind of simulations is not possible
>>without a
>> modification of the forcefiel
On 2/7/13 2:29 PM, Davide Mercadante wrote:
Thank you Justin,
I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?
If you're looking to unfold secondary structure eleme
Thank you Justin,
I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?
Thanks.
Cheers,
Davide
On 7/02/13 8:09 PM, "Justin Lemkul" wrote:
>
>
>On 2/7/13 1:44 PM, Davide
On 2/7/13 1:44 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in o
Dear Justin,
Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in order to reach a simulated
time where the pull o
On 2/7/13 5:20 AM, Davide Mercadante wrote:
Dear All,
I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions
Dear All,
I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions NA+ and CL-.
After the equilibration I start a
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