[gmx-users] about the frame selection

[Anirban]

On Tue, May 15, 2012 at 11:26 AM, rama david <ramadavidgroup at gmail.com>wrote:

> Hi Gromacs Users ,
>    I simulated a  4 peptide in a box .
>  After completion of 30 ns simulattion , I extract
> the particular time frame 29000 ps of my interest.
>  Now I want these  frame for  my next simulations
> study ..
> In one simulation I want to keep the box size same as the
> mentioned in extracted pdb  and in another one  I need to change the size
> of box to
> 70 70 70
>
>
> REMARK    GENERATED BY TRJCONV
> TITLE     Protein in water t= 29000.00000
> REMARK    THIS IS A SIMULATION BOX
> CRYST1   45.096   45.096   45.096  90.00  90.00  90.00 P 1           1
> MODEL        1
>
>   So  my queries are like
>
> 1. Should I used the extracted frame directly for further study or
>     I need to remove the periodicity...??????
>

I think its better to remove the periodicity when you are going to start a
fresh simulation with this protein.


>
>  2 . to change the box size how to proceed ??
>          Should I delete the line manually and adjust the box size????
>

You can change the box dimensions with editconf using the -box (desired
dimensions) option.

-Anirban

>
>
> All suggestion are welcome ...
>
>
> Than you in advance
>
> rama david
>
>
>
>
>
>
>
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