[gmx-users] au--protein separate equilibration

[Justin Lemkul]

On 1/17/13 2:48 PM, fatemeh ramezani wrote:
> Dear Justin thanks for your reply and,
> Please help me to correct the settings of .mdp files step by step .

I did that in my previous reply.

> By these em.mdp files if I freeze only protein for the first time and after
> minimization I use the result .pdb file for second step of minimization that
> I freeze AU atoms in it, minimization would be true?
>

I don't understand the purpose of freezing anything during EM; that sort of 
defeats the purpose of optimizing geometry.  You can approach your problem 
however you see fit.

-Justin

>  > title              =  n.pdb
>  > cpp                =  /lib/cpp
>  > define              =  -DFLEXIBLE
>  > constraints        =  none
>  > integrator       =  steep
>  > dt                  =  0.002
>  > nsteps              =  40000
>  > ;constraint_algorithm  = shake
>  > ;shake_tol          = 0.0001
>  > ;nstenergy          =  10
>  > ;nstxtcout          =  10
>  > ;nstlist            =  5
>  > ns_type            =  grid
>  > rlist              =  1
>  > coulombtype        =  PME
>  > rcoulomb            =  1
>  > rvdw                =  1.2
>  > fourierspacing      =  0.12
>  > fourier_nx =  0
>  > fourier_ny          =  0
>  > fourier_nz          =  0
>  > pme_order          =  6
>  > ewald_rtol          =  1e-5
>  > optimize_fft        =  yes
>  > ;      Energy minimizing stuff
>  > emtol              =  1000.0
>  > emstep              =  0.01
>  > freezegrps          =  Protein
>  > freezedim          =  Y Y Y
>  > comm_mode          =  None
>  >
>
>  > 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain:
>  > title              =  n.pdb
>  > cpp         =  /lib/cpp
>  > define              =  -DFLEXIBLE
>  > constraints        =  none
>  > integrator          =  steep
>  > dt                  =  0.002
>  > nsteps              =  40000
>  > ;constraint_algorithm  = shake
>  > ;shake_tol          = 0.0001
>  > ;nstenergy          =  10
>  > ;nstxtcout          =  10
>  > ;nstlist            =  5
>  > ns_type            =  grid
>  > rlist              =  1
>  > coulombtype        =  PME
>  > rcoulomb       =  1
>  > rvdw                =  1.2
>  > fourierspacing      =  0.12
>  > fourier_nx          =  0
>  > fourier_ny          =  0
>  > fourier_nz          =  0
>  > pme_order          =  6
>  > ewald_rtol          =  1e-5
>  > optimize_fft        =  yes
>  > ;      Energy minimizing stuff
>  > emtol              =  1000.0
>  > emstep              =  0.01
>  > freezegrps          =    AU  AUI    AUC
>  > freezedim          =  Y Y Y  Y Y Y  Y Y Y
>  > comm_mode          =  None
>

-- 
========================================

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

========================================