VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Mon Oct 07 2019 - 02:26:32 CDT

Hi,
Your protein can't be in the center of the box every time, it can move
freely around . if you want your protein to be in the center of the box, I
suggest you do wrapping after a run by the following command

"pbc wrap -all -compound fragment -center com -centersel protein "

https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#x1-180006 I suggest
you read this for more information.

On Mon, Oct 7, 2019 at 10:49 AM Santhosh Ranga <
santhoshchemistry528_at_gmail.com> wrote:

> Dear Team_at_NAMD,
>
> I am Dr. Santosh Ranga, a postdoctoral fellow, in the department of
> chemistry, the Indian Institute of Technology (IIT B), Mumbai.
>
> I was trying to perform initial MD simulations systematically using NAMD.
> My query is that I want to allow the protein to interact with the solvent
> (water), but at the same time, it should be at the center of the box.
>
> fixedAtoms on
>
> fixedAtomsFile myfixedatoms.pdb ;# flags are in this file
>
> fixedAtomsCol B ;# set beta non-zero to fix an atom
>
>
> When I include these keywords in the conf file, my protein is frozen in
> the center, not given flexibility.
>
> My idea is that I want to give the flexibility for both solute and the
> solvent being protein at the center.
>
> Please help me what the changes I have to do in the PDB file or conf file
> so that I would be able to see what is happening with time are.
>
> Since I am new to MD simulations using NAMD, educate me with your
> knowledge.
>
> I appreciate your patience.
>
>
> Thank you,
>
> IPDF, IIT Bombay,
>
> India.
>

On Mon, Oct 7, 2019 at 10:49 AM Santhosh Ranga <
santhoshchemistry528_at_gmail.com> wrote:

> Dear Team_at_NAMD,
>
> I am Dr. Santosh Ranga, a postdoctoral fellow, in the department of
> chemistry, the Indian Institute of Technology (IIT B), Mumbai.
>
> I was trying to perform initial MD simulations systematically using NAMD.
> My query is that I want to allow the protein to interact with the solvent
> (water), but at the same time, it should be at the center of the box.
>
> fixedAtoms on
>
> fixedAtomsFile myfixedatoms.pdb ;# flags are in this file
>
> fixedAtomsCol B ;# set beta non-zero to fix an atom
>
>
> When I include these keywords in the conf file, my protein is frozen in
> the center, not given flexibility.
>
> My idea is that I want to give the flexibility for both solute and the
> solvent being protein at the center.
>
> Please help me what the changes I have to do in the PDB file or conf file
> so that I would be able to see what is happening with time are.
>
> Since I am new to MD simulations using NAMD, educate me with your
> knowledge.
>
> I appreciate your patience.
>
>
> Thank you,
>
> IPDF, IIT Bombay,
>
> India.
> 

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*