[gmx-users] (no subject)

[Nguyen Hoang Phuong]

> Hi all,
> I am a new GROMACS user and I am trying to have a NMA of a protein. I would like to make you some questions.
>  Which parameters do you recommend to minimized for a further Normal Mode Analysis? I'd apprecite a lot if someone could send to me an example of the .mdp files. Might I do the energy minimization in water or in vacuum?
> If the protein is charged, migth I include counter-ions for the minimization??
> How large would be the Hessian matrix if the protein has 3500 atoms aprox?
> Thanks in advance for your kind attention,
> Best regards,
>
> Monica
>
>

Hi,

first, you have to use double precision.
Here is an example of mdp file.
title                    = protein in water
cpp                      = /lib/cpp
include                  = -I../top
define                   = -DFLEX_SPC
integrator               = cg
emtol                    = 0.000001
emstep                   = 0.000001
nstcgsteep               = 100
nsteps                   = 500000
nstxout                  = 50
xtc_grps                 = Protein
energygrps               = Protein
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.4
vdwtype                  = Shift
coulombtype              = PME
rcoulomb                 = 1.4
rvdw                     = 1.4

in vacuum, you can easily get the mimimum energy structure but in
water it will take a lot of time. You can look at the value of Fmax which
is printed out for every step. If Fmax<10^5 then you may have the optimal
structure. To make sure, you can also look at the eigenvalues of the
Hessian. If all values are positive then everything is OK. The size of
Hessian is (3N x 3N) where N is the number of atoms. It will take a lot of
time to diagonalize such matrix. However, if you are interested in some
normal modes then only sub-matrix of the Hessian is needed to be
diagonalized.

Phuong