Liu, Liang wrote:
Thanks for the information.
It looks the pdb2gmx can generate the posre.itp file and what I use
is "pdb2gmx -ignh -ff amber03 -f *.pdb -o *.gro -p *.top -water spce".
The file shows:
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained."
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
<snip>
It is unnecessary to paste this information.
So how to adjust the force constraint to the harmonic poteitial E =
k(r-r0)^2, with different values of k?
The file format is discussed in the manual, Chapter 4. You can alter the force
constants in x, y, and z dimensions independently. The force constants are
listed in the fx, fy, and fz columns.
I am totally a new user of Gromacs, even MD simulation. Please help,
I would suggest you familiarize yourself with Gromacs capabilities, file
formats, and workflows by working through any of the multitude of tutorials
linked on the Gromacs website.
-Justin
Thanks a lot.
On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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