[gmx-users] cant load trajectory, low memory

[abhisek Mondal]

Hi,

I'm going with it.

I still have a question. If I reconstruct the system (stripping the solvent
and thus making smaller box size) I need to go through NVT>NPT
equilibrations again. This part I got it.
The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
will do ?
What is the difference between running npt simulation with npt.mdp and
npt_umbrella.mdp ?

Please help me to catch up here.

Thank you.

On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/24/17 12:56 PM, abhisek Mondal wrote:
>
>> Hello,
>>
>> I'm using the configurations generated by pulling run to re-box >
>> resolvate
>>
>>> ion addition > EM > npt_umbrella(10ns) and forward.
>>>
>>
>> So, please clarify me something. Am I following correct path ? Should I
>> have given a npt equilibration step prior to npt_umbrella step ?
>>
>>
> Yes, as Mark said, you're essentially building all new simulation systems.
> Since this is part of an umbrella sampling series, be sure you're getting
> the same (or at least, very similar) number of water molecules in each box.
>
> -Justin
>
> Thank you.
>>
>> On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> I already answered that. You're effectively starting again, so do that.
>>>
>>> Mark
>>>
>>> On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal <abhisek.mndl at gmail.com>
>>> wrote:
>>>
>>> Ok, I got it this time.
>>>> But what kind of equilibration I'm to perform on these stripped
>>>>
>>> structures.
>>>
>>>> Should I perform normal NPT equilibration as done before generating
>>>> configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c
>>>>
>>> conf0.gro
>>>
>>>> -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
>>>> page) and followed by mdrun step ?
>>>>
>>>>
>>>> ....
>>>
>>>