[gmx-users] Water molecule can not be settled

[zeineb SI CHAIB]

Dear Mark, 

Again, thank you very much for your orientation. 

I suceeded in running a minimisation in vaccuo (just after pdb2gmx) with the following command line:

gmx mdrun -ntmpi 1 -v -deffnm protein_invacuo -s protein_invacuo.tpr

The mdp parameters were:

integrator = steep  
nsteps = 1500  
emtol = 1000.0   
emstep = 0.01   
energygrps    = system

pbc         = no
nstlist = 0
ns-type = simple
rlist       = 0

cutoff-scheme = group
coulombtype              = cut-off
rcoulomb                 = 0
vdw-type                 = Cut-off
rvdw                     = 0

During minimisation, I had no error and Steepest Descents converged to Fmax < 1000 in 389 steps
Potential Energy  = -8.8386008e+04
Maximum force     =  9.7354883e+02 on atom 3974
Norm of force     =  4.0786911e+01

However,
 when I visualised the .gro file generated after minimisation, in VMD, 
It can't correctly display the parametrized molecule (THF). For example,
 for a representation in licorice, I had this (right and left are HEM 
and in the center is my THF!!):

https://www.dropbox.com/s/xrxw473pywbiz1s/THG_problem.png?dl=0

NB: my input structure has been obtained by homology modelling using MODELLER but I don't think that the problem is here because I already run an MD of 5ns with this structure but I added the topology of THF manually (like in bevanlab tutorial)!?

What do you think happened?

Regards.

Zeineb