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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
