VMD-L Mailing List

From: Ebru Çetin (ebrucetin_at_sabanciuniv.edu)
Date: Sat Oct 23 2021 - 03:51:17 CDT

Hi Ryan,

I think this is a namd problem. Your system may not be equilibrated well.
For the solution, you can start at a lower temperature (280 K) at the NVT
ensemble and increment it step by step. This way your density will become
uniform and then you can start the NPT simulations.

I hope this helps,

Regards,

Ebru

On Sat, Oct 23, 2021 at 10:06 AM Ashar Malik <asharjm_at_gmail.com> wrote:

> Hi,
>
> Unfortunately, I cannot be of any help in this regard.
> I have never encountered this problem before and if I did, I would
> actually run the MD simulation again.
>
> As I mentioned earlier as well, it is my hunch that the behaviour you are
> seeing is because of periodic boundaries not being set up correctly.
>
> I am not familiar with any steps that can fix your problem, but then again
> I am not an expert.
>
> Perhaps you could wait here for more input from others who are more
> experienced. both to confirm the cause of the problem and if someone might
> have seen this behaviour they might suggest a solution.
>
> Sorry for not being able to suggest a fix.
>
> Regards,
> Ashar
>
> On Sat, Oct 23, 2021 at 2:01 PM Ryan Woltz <rlwoltz_at_ucdavis.edu> wrote:
>
>> Hi Ashar,
>>
>> Yes, with your explanation I'm certain the initial boundaries is
>> ~145. Sorry for the confusion but the naming is different with files coming
>> out of Charmm-gui with the second email being initial config file in step1
>> of the setup. Charmm-gui goes through 5 stages of setup. The
>> protein +membrane is setup in step3 which is where I enter the "145" number
>> and it confirms the protein can fit in this size.
>>
>> The files that do the initial run of MD is a .inp (input) file
>> and I found this line in here.
>>
>> cellBasisVector1 $a 0.0 0.0; # vector to the next image
>> cellBasisVector2 $d $b 0.0;
>> cellBasisVector3 0.0 0.0 $c;
>> cellOrigin 0.0 0.0 $zcen; # the *center* of the cell
>>
>> So in the previous response the lines set a,b,c I think this is
>> how these variables are being used. From file step5_input.str. These input
>> values are again
>>
>> set a 141.104004
>> set b 141.104004
>> set c 144.858064
>>
>> so 141, 141, and 145. apologies for the misunderstanding of terms
>>
>> If the values are used as boundaries for your entire system
>> (i.e., membrane + water) and the minmax result you provided earlier - then
>> yes. Your periodic setup is smaller than your entire system which can
>> explain why your "jumps" appear with the system instead of on edges.
>>
>> How do you recommend we proceed from here? I've been trying to
>> wrap things using the protein as my selection and focusing on that but is
>> there a way to wrap by size dimensions you calculated? (180,188,158) I know
>> this will probably be very time consuming to do it this way, correct?
>>
>> Thanks for your patience and help,
>>
>> Ryan
>>
>> On Fri, Oct 22, 2021 at 10:43 PM Ashar Malik <asharjm_at_gmail.com> wrote:
>>
>>> Hi Ryan
>>>
>>>
>>>> {"systype":"bilayer","dimensions":["145.078088","145.078088","144.858064","90.0","90.0","90.0"],"input":["namd"],"forcefield":{"type":"c36m","files":["default"],"custom":[]},"hmr":false}
>>>>
>>>>
>>> Again not familiar with the contents of the string above and how each of
>>> the values is being used.
>>> I am also not familiar with how you set up your system.
>>>
>>> Taking your system as an example a typical workflow will look
>>> something like this
>>>
>>> A membrane + protein system is constructed which is then minimized
>>> followed by solvation/ionization, minimized again and then the system goes
>>> into MD.
>>>
>>> At each step when things are being moved or added your system size can
>>> vary.
>>>
>>> Just before MD, you have to know the system size. The way I am familiar
>>> with MD is through the use of a config file which contains line-by-line a
>>> collection of variables that you can change the value of. Programs like
>>> NAMD will then read that list and the explicit values from the config file
>>> will replace system defaults. Some values have no defaults and must be
>>> provided.
>>>
>>> e.g., see here
>>> https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
>>>
>>> Within the description listed in the page above you will notice 4 lines--000000000000d5f39f05cf013b01--