[gmx-users] Normal mode analysis
Smith, Micholas D.
smithmd at ornl.gov
Wed Feb 26 14:40:28 CET 2020
Where did you obtain your PDB? Is this a known crystal structure or other experimentally derived structure or is it a homology model? Sometimes the initial structures have minor artifacts that make energy minimization difficult. Perhaps a short-restrained MD simulation (10ps perhaps) with 10kJ/mol position restraints could remove these artifacts and then you can re-minimize and run your normal mode calculation.
-Micholas
===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________
From: Katrien Clerx <katrien.clerx at student.kuleuven.be>
Sent: Wednesday, February 26, 2020 8:29 AM
To: Smith, Micholas D. <smithmd at ornl.gov>; gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: [EXTERNAL] RE: [gmx-users] Normal mode analysis
My structure does not contain any ions. Here are the commands that I used:
gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water tip3p -ignh
gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5
gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr
gmx_d mdrun -deffnm cg -v
gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr -maxwarn 1
gmx_d mdrun -deffnm bfgs -v
gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr
The used mdp files:
cg.mdp :
; Parameters describing what to do, when to stop and what to save
integrator = cg ; Algorithm (cg= Conjugate Gradient minimization)
emtol = 0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm
emstep = 0.1 ; Energy step size
nsteps = 500000 ; Maximum number of
(minimization) steps to perform
nstcgsteep = 1000
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
cutoff-scheme = verlet
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 1.0 ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2; Short-range Van der Waals cut-off
fourierspacing = 0.12
pme_order = 4
ewald_rtol =1e-09
epsilon_surface = 0
pbc = xyz ; Periodic Boundary Conditions (yes/no)
bfgs.mdp:
;mdp for l-bfgs energy minimization
define = -DFLEXIBLE
constraints = none
integrator = l-bfgs
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
cutoff-scheme = verlet
nstlist = 10 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
coulombtype = Reaction-Field
coulomb-modifier = potential-shift ; Treatment of long range electrostatic interactions
rcoulomb-switch = 1.0
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
fourierspacing = 0.12
pme_order = 4
epsilon_surface = 0
ewald_rtol = 1e-9
pbc = xyz ; Periodic Boundary Conditions (yes/no)
;
; Energy minimizing stuff
;
emtol = 0.0
emstep = 0.0001
nstcgsteep = 1000
nbfgscorr = 100000
nsteps = 500000
nm.mdp:
; Parameters describing what to do, when to stop and what to save
define = -DFLEXIBLE
integrator = nm ; Algorithm (normal mode)
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
cutoff-scheme = verlet
nstlist = 10 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions
coulomb-modifier = potential-shift
rcoulomb-switch = 1.0
rcoulomb = 1.2 ; Short-range electrostatic cut-off
vdwtype = Cut-off
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2; Short-range Van der Waals cut-off
fourierspacing = 0.12
pme_order = 4
ewald_rtol =1e-09
epsilon_surface = 0
pbc = xyz ; Periodic Boundary Conditions (yes/no)
nsteps = 10000000
From: Smith, Micholas D.<mailto:smithmd at ornl.gov>
Sent: woensdag 26 februari 2020 14:10
To: Katrien Clerx<mailto:katrien.clerx at student.kuleuven.be>; gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] Normal mode analysis
Hmmm....
How did you prepare the structure? Also, attachments are stripped from emails to the mailing list, can you please provide your mdp file as plain text in your reply.
===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Katrien Clerx <katrien.clerx at student.kuleuven.be>
Sent: Wednesday, February 26, 2020 7:52 AM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis
Yes I used double precision for everything.
-Katrien
From: Smith, Micholas D.<mailto:smithmd at ornl.gov>
Sent: woensdag 26 februari 2020 13:39
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] Normal mode analysis
Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build.
-Micholas
===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Katrien Clerx <katrien.clerx at student.kuleuven.be>
Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: [EXTERNAL] [gmx-users] Normal mode analysis
?Hello,
Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3.
But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00.
I used the attached mdp-files.
Am I doing something wrong? If so, what am I doing wrong and how can I fix it?
Kind regards,
Katrien
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