Please keep the discussion on the gmx-users mailing list.
On 1/29/13 12:20 PM, Masomeh Dehghani wrote:
Dear Justin
Have a nice time.
Thank you for your reply.
I did my simulation with distance restraint again.(my system has 6
water molecule, I want to imose distance restarint between oxygen atoms with
0.42 nm together. 1,4,7,10,13,16 are oxygen atoms in system)
disre.itp:
[ distance_restraints ]
;ai aj type index type low up1 up2 fac
1 4 1 1 6 0.42 0.43 0.44 1.0
1 7 1 1 6 0.42 0.43 0.44 1.0
1 10 1 1 6 0.42 0.43 0.44 1.0
1 13 1 1 6 0.42 0.43 0.44 1.0
1 16 1 1 6 0.42 0.43 0.44 1.0
4 7 1 1 6 0.42 0.43 0.44 1.0
4 10 1 1 6 0.42 0.43 0.44 1.0
4 13 1 1 6 0.42 0.43 0.44 1.0
4 16 1 1 6 0.42 0.43 0.44 1.0
7 10 1 1 6 0.42 0.43 0.44 1.0
7 13 1 1 6 0.42 0.43 0.44 1.0
7 16 1 1 6 0.42 0.43 0.44 1.0
10 13 1 1 6 0.42 0.43 0.44 1.0
10 16 1 1 6 0.42 0.43 0.44 1.0
13 16 1 1 6 0.42 0.43 0.44 1.0
my topology file:
; Include Distance restraint file
#ifdef DISRE
#include "disre.itp"
#endif
em.mdp file:
define = -DDISRE
; DISTANCE RESTRAINTS
disre = simple
disre_weighting = equal
disre_fc = 20
disre_mixed = yes
disre_tau = 10
nstdisreout = 100
and also add these lines :
; Distance restraints
define = -DDISRE
; DISTANCE RESTRAINTS
disre = simple
disre_weighting = equal
disre_fc = 20
disre_mixed = yes
disre_tau = 10
nstdisreout = 100
to pr.mdp and md.mdp files.
I didn't have any erorr,
but after 500 ps , I checked output and saw 6 water molecules were
far from together.
I don't know what I have to do.
Do you have your topology correctly set up such that the water molecules to
which you are applying restraints are unified in a single [moleculetype]?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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