[gmx-users] about the frame selection
reach.anirban.ghosh at gmail.com
Tue May 15 08:08:59 CEST 2012
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
> All suggestion are welcome ...
> Than you in advance
> rama david
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