VMD-L Mailing List

From: Ryan Woltz (rlwoltz_at_ucdavis.edu)
Date: Fri Oct 22 2021 - 21:57:27 CDT

Hi Ashar,

          I don't think they match up, but I'm not exactly sure with the
exact commands. With VMD returned information:

$ minmax 0
{-104.74568176269531 -113.04422760009766 -86.82054138183594}
{76.17849731445313 75.81551361083984 72.08464813232422}

         in file the namd file step5_input.str I found this:

set a 141.104004
 set b 141.104004
 set c 144.858064

         I'm not sure if these are the correct numbers you are looking for.
In charmm-gui when setting up the system I did enter 135-145 for the
initial size estimate for each side depending on the system so I think it
matches up.

Was this what you were looking for? Any other information I can provide you
with that would help in your assistance?

Thank you,

Ryan

On Fri, Oct 22, 2021 at 7:35 PM Ashar Malik <asharjm_at_gmail.com> wrote:

> Quick question(s).
>
> What is the size of your system. Measure this by opening up the original
> system in VMD, from which you start your simulation, and measuring using
> the min max command or manually.
>
> In the MD Config file what is the size of the system.
>
> Do these two sizes match up?
>
>
> On Sat, 23 Oct 2021 at 4:38 AM, Ryan Woltz <rlwoltz_at_ucdavis.edu> wrote:
>
>> Dear Community,
>>
>> From other posts I know this problem has been addressed a few
>> times for the protein, but when I solve the protein issue I find other
>> problems. I have a membrane embedded channel and I'd like to look at how
>> the protein interacts with different lipids. I have 2 systems 1) POPC only
>> 2) 90% POPC/10% PIP2 (SAPI24) in the lower leaflet. Very basically I want
>> to track various lipid distances/packing/velocities around specific amino
>> acids. I have two problems.
>>
>> 1) lipids that I want to measure distances with are jumping to the
>> opposite side of the box (not quite another box ~95-101 angs in a 135 ang
>> box)
>>
>> 2) In half of the simulations I also have peptide jumping (solved with
>> commands below) but when I correct for this using the pbc commands the
>> water freely jumps to other boxes leaving only a couple waters in the
>> original box by the end of the simulation. This is a problem as a big part
>> of the simulation is water interaction with the Selectivity filter region
>> of the channel. Also still problems with lipid jumping from problem 1.
>>
>> I've asked around some labs and everyone is aware of the problem but
>> nobody has a concrete solution beyond "try different variations until it
>> works". I was wondering if anyone has a script or tips on how to adjust my
>> commands to get everything into the same box.
>>
>> restypes that are jumping.
>> water - TIP3
>> POPC - POPC
>> PIP2 - SAPI24
>>
>> Current commands used (I use -bondlist to bond everything from what I
>> understand)
>>
>>
>> -
>>
>> pbc join fragment –bondlist –now
>> -
>>
>> pbc wrap –centersel protein –center com –compound fragment –all
>> -
>>
>> pbc unwrap
>>
>>
>> Thank you for any help you can give,
>>
>> Ryan Woltz
>>
>