Thanks for your answer. I hope I did not catch your points well. So, you mean I can use 'gen_vel = no' for the md runs (MD without position restraints, after the completion of PR run with position restarints) my procedure as follows......
EM ---> PR(300ps @ 300K) ----> MD (30ps @ 80K. no postion restraints)---> MD (30 ps @ 100K, no postion restraints ) ---> MD (30 ps @ 200K, no postion restraints) ----> relaxation MD(250ps @ 300K, no postion restraints) ----> final MD (300K, no postion restraints) After Energy minimization, I apply position restarints and generate new velocities at 300K. I take the output of PR run as input to the next MD run which started at 80K ( no position restraints from now). And also from here onwards i dont generate any new velocities, but with the velocities which are written in the previous runs. Looking forward for your reply. Please let me know Thanks again Gajula > Dear Gromacs Users, > > I am getting different results for simulations with " gen_vel=yes" and > "gen_vel= no". This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random number seed. What you want to do, is after equilibration, be sampling from the correct ensemble. > I have generated velocities only for PR MD at 300K. after that I set ' > gen_vel= no ' in mdp file. After the position restrained MD , I slowly > increased the temparature from 80K , 100K , 200K and last 300K. (with > 'gen_vel=no' for all MD) > Is it correct? Because I read both 'yes' and 'no' as possibilites in some > references. Iam bit confused which to use for exact simulations. Personally, I don't think the practice of velocity reassignment in incremental heating while using position restraints is demonstrably better than not using reassignment in incremental heating. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
