On 27/09/2011 12:49 PM, Liu, Liang wrote:
Thanks.
Is this position restraint same to the one "Position Restrained MD". I
see some tutorial shows there are always three step to perform a
simulation: Energy minimization, Position Restrained MD and MD Simulation.
"Always" is too strong, but this is common.
Is it possible to fulfill the position restraint during Position
Restrained MD? Thanks.
Yes, hence the name. How well they can be fulfilled depends on the
initial and simulation conditions.
Mark
On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Liu, Liang wrote:
Firstly I want to thank for your reply, yes, it should be
position restraint.
I don't know how to reply in the thread, actually that was my
first post. Therefore I have to ask you here, hope it also
work to you.
Simply reply to the message. The discussion needs to stay on the
list. The members are not private tutors.
My question is how to perform a position restraint simulation
with the heavy atom constrained to its initial position by a
harmonic potential E=k(r-r0)^2,
which changes with k equal to 0, 10, 20, ..., 90, 100, and so on?
You can adjust the force constant in the posre.itp file. There is
no automated way of decreasing or increasing a restraint;
independent simulations must be run on the different topologies.
-Justin
Thanks, and any helps will be highly appreciated.
--
Best,
Liang Liu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
Best,
Liang Liu
--
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
