Steven Neumann wrote:
Dear Gmx Users, Dear Justin
I am wondering which approach for generating velocities in protein or
protein-ligand system is a proper one:
a)
NVT gen_vel = yes
gen_temp=298
gen_seed=-1
NPT gen_vel=no
MD gen_vel=no
b)
NVT gen_vel = yes
gen_temp=298
gen_seed=-1
NPT gen_vel=no
MD gen_vel = yes
gen_temp=298
gen_seed=-1
As I always used the approach a) I saw in Justin's tutorial (Protein and
ligand) b). However, in protein in water tutorial he used the approach
a). I am confused, can you please help?
There was a typo in the tutorial. Approach (a) is correct. After
equilibration, regenerating velocities destroys the equilibrated ensemble.
I have fixed the tutorial's .mdp file. Thanks for pointing out the mistake.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
