[gmx-users] Simulated annealing

jayant james jayant.james at gmail.com
Fri Mar 20 22:45:40 CET 2009

Hi !
I am attempting to do a simulated annealing and running into problem.
Let me give a introduction to my system. I have a segment of a protein that
was not crystallographyically resolved, but was later resolved by NMR.
So I ligated the NMR structure to the crystal structure  and in an attempt
to find the correct orientation of the NMR segment in the crystal structure
I planned to do a simulated annealing run specifically to this ligated NMR
segment. Having ligated this NMR segment to the crystal structure I gave the
pdb2gmx command, then created a box, filled it with water and performed a
distance restrained energy minimization (wherein I input some FRET distances
as distance restraints). Its all fine till this step. Now I create an index
group that has the NMR group as the third group in the temperature coupling,
the other two are Protein and Non-Protein. when I run the grompp to start a
simulated annealing run I get a message stating that the NMR group's atoms
are also found in the Protein group. Gromacs is right in detecting this
problem. As I cannot have the same amino acids in 2 different groups which
are coupled to two different temperatures. So how am I to attempt this
simulated annealing because the program does not want to have the NMR
group present in the Protein group?
So say I delete the NMR segment that was appended to the crystal structure
how and which stage do I integrate the NMR group that I wanted to perform
the simulated annealing on, into the system?

*The pr.mdp file is as below*

; Berendsen temperature coupling is on in two groups

Tcoupl              = Berendsen

tc-grps               =  Protein   Non-Protein   NMR-group

tau_t               =  0.1           0.1           0.1

ref_t               =  300           300           300

; Energy monitoring
energygrps      =  Protein       Non-Protein    NMR-group
; Pressure coupling is not on

Pcoupl              =  parrinello-rahman

tau_p               =  0.5

compressibility     =  4.5e-5

ref_p               =  1.0

; Generate velocites is on at 300 K.

gen_vel             =  yes

gen_temp            =  300.0

gen_seed            =  173529




;simulated annealing

;Type of annealing form each temperature group (no/single/periodic)

annealing       = no    no  single


;Number of annealing points to use for specifying annealing in each group

annealing_npoints      0  0  9


; List of times at the annealing points for each group

annealing_time       =  0 25 50 75 100 125 150 175 200

; Temp.at each annealing point, for each group.
annealing_temp      =  300 350 400 450 500 450 400 350 300

*The error messge is given below*

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#

checking input for internal consistency...

calling /usr/bin/cpp...

processing topology...

Generated 279 of the 1225 non-bonded parameter combinations

Excluding 3 bonded neighbours for Protein_D 1

Excluding 2 bonded neighbours for SOL 72948

Excluding 1 bonded neighbours for NA+ 214

Excluding 1 bonded neighbours for CL- 207

processing coordinates...

double-checking input for internal consistency...

Velocities were taken from a Maxwell distribution at 300 K

renumbering atomtypes...

converting bonded parameters...

#   G96BONDS:   4588

#  G96ANGLES:   6638

#      PDIHS:   2521

#      IDIHS:   2044

#       LJ14:   7634

#     DISRES:   22

#     SETTLE:   72948

initialising group options...

processing index file...

WARNING 1 [file "new.top", line 28039]:

  T-Coupling group Protein has fewer than 10% of the atoms (4550 out of


  Maybe you want to try Protein and Non-Protein instead?

WARNING 2 [file "new.top", line 28039]:

  T-Coupling group Non-Protein has fewer than 10% of the atoms (2 out of


  Maybe you want to try Protein and Non-Protein instead?


Program grompp, VERSION 3.3.3

Source code file: readir.c, line: 843

Fatal error:

Atom 2589 in multiple T-Coupling groups (1 and 3)

*The commands that I use are given below*
#pdb2gmx -f start.pdb -p new  -o new -ignh -merge

#creating a box and addition of water molecules

#editconf -f new.gro -o out -c  -princ -d 2.2

#genbox -cp out -cs -o check

#editconf -f check  -o check.pdb

#rasmol check.pdb

#Energy minimization and addition of ions to neutralise the system

#grompp -f em.mdp -c check -p new.top -o em.tpr

#genion -s em.tpr -o next  -p new -random -g -neutral -conc 0.15 #pname -Na
-np 13

#editconf -f next.gro -o next.pdb

#rasmol next.pdb

#option 13 for SOL

#Running the EM. Here change the Na to NA+ in topology  file and I/P *.gro

#grompp -f em.mdp -c next.gro -p new.top -o em.tpr

#mdrun -v -s em -x em -o em -c em.gro &

#editconf -f em.gro -o em.pdb

#rasmol em.pdb

*This is where the problem begins*

#Running MD.

grompp -f pr.mdp -c em.gro -o pr.tpr -p new.top -n index

#mdrun -s pr -e pr -g md -o traj.trr -c pr.gro &


#tpbconv -s ../pr.tpr -f 300.xtc  -e ../ener.edr -o 1ns.tpr -until 1000

#mdrun -s 1ns.tpr -o 1ns.trr &

Jayasundar Jayant James

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090320/c4ccc752/attachment.html>

More information about the gromacs.org_gmx-users mailing list