On 1/28/13 2:10 PM, Masomeh Dehghani wrote:
Dear users
I have 6 water molecules ,I want to constraint the distance between 6 oxygen
atoms in 0.42 nm from together.I read GROMACS manual but I had fatal erorr.
Here there is disres.itp file:
; Include Distance restraints file
#ifdef DDISRES
#endif
[ distance_restraints ]
;ai aj type index type' low up1 up2 fac
1 4 1 1 1 0.42 0.42 0.42 2.0
1 7 1 2 1 0.42 0.42 0.42 2.0
1 10 1 3 1 0.42 0.42 0.42 2.0
1 13 1 4 1 0.42 0.42 0.42 2.0
1 16 1 5 1 0.42 0.42 0.42 2.0
I doubt this approach will work. Note the functional form provided in the
manual - if your molecules deviate, I doubt that mdrun will know how to actually
calculate the energy associated with the deviation. You need to supply a range
of values within which the distances may oscillate.
my topology file:
; Include Distance restraint file
#ifdef DISRES
#include "disres.itp"
#endif
my em.mdp
define = -DDISRES
disres = simple
error
WARNING 1 [file em.mdp, line 19]:
Unknown left-hand 'disres' in parameter file
The keyword is "disre," not "disres."
http://manual.gromacs.org/online/mdp_opt.html#nmr
-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
========================================
--
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
