On Tue, May 15, 2012 at 11:26 AM, rama david <ramadavidgr...@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 > > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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