[gmx-users] questiones about dihedral restrain

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Sun Jun 17 10:33:51 CEST 2012

Dear All:

I am using gromacs4.5.3 to do umbrella sampling simulation of the residue side chain dihedrals. I used the dihedral restrain method described in the mannual to restrain the dihedral values. The method we used is described as follows:
we first added the following parameters in the *.top file immediately after the parameters of the protein:

[ dihedral_restraints ]
; ai   aj    ak    al  type  label  phi  dphi  kfac  power
   4    6    9    12     1   1    180     0     1   2
Then we added the following parameters in the *.mdp file :

; dihedral restraints
dihre               =  yes
dihre_fc            =  1000     ; or whatever value you desire
dihre_tau           =  0.0
nstdihreout         =  50

Then we used the following commond to generate the tpr file:

grompp -f ourfile.mdp -c ourfile.gro -p ourfile.top -o ourfile.tpr

After the simulations, we used the g_angle commond to calculate the distribution of the dihedral angels:

g_angle_d -f oufile.trr  -n ourfile.ndx  -od ourfile.xvg -type dihedral

However, we found that in the simulation results, the dihedral was not restrained as we expected. The dihedral angles distrbuted in a wide range around its initial values and when larger force constant were applied the distribution was not affected. It seemed that the externial forces we assigned was not applied on the residue.

The other parameters we used was the same with that we used in un-restrained simulations. Could anyone help me with this problem? Did I used the wrong parameters or are there any other wrong in my simulations?

Thanks in advance.

Best Regards


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