[gmx-users] Continuation=yes From?

2011-05-02 Thread mohsen ramezanpour
Dear Dr.Justin Regarding Umbrella Sampling tutorial: The CONTINUATION option in md_umbrella.mdp is YES, and you have noticed : From NPT I can't understand it's reason correctly! we run a NPT and then Pulling, then extracted some configurations from pull.trr file. I think we must continue from

Re: [gmx-users] Continuation=yes From?

2011-05-02 Thread Justin A. Lemkul
mohsen ramezanpour wrote: Dear Dr.Justin Regarding Umbrella Sampling tutorial: The CONTINUATION option in md_umbrella.mdp is YES, and you have noticed : From NPT I can't understand it's reason correctly! This is a meaningless comment. It was left there from copying and pasting files

Re: [gmx-users] Continuation=yes From?

2011-05-02 Thread mohsen ramezanpour
Dear Dr.Justin Thank you for your reply My is Protein-ligand,It is have the same conditions as tutorial.I did pull ligand in the z direction. Actualy I found your note about gen_vel ,but I didn't any about Continuation! You are right,But there is another problem: You have not used any-t

Re: [gmx-users] Continuation=yes From?

2011-05-02 Thread Justin A. Lemkul
mohsen ramezanpour wrote: Dear Dr.Justin Thank you for your reply My is Protein-ligand,It is have the same conditions as tutorial.I did pull ligand in the z direction. Actualy I found your note about gen_vel ,but I didn't any about Continuation! Not that specific keyword, no, but I do

Re: [gmx-users] Continuation=yes From?

2011-05-02 Thread mohsen ramezanpour
Thank you for your detailed axplain I understood completely On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.Justin Thank you for your reply My is Protein-ligand,It is have the same conditions as tutorial.I did pull ligand in the