Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

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 
Sent: Wednesday, February 26, 2020 8:29 AM
To: Smith, Micholas D. ; gmx-us...@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   = 50; 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  = 10

nsteps   = 50





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-ra

Re: [gmx-users] Normal mode analysis

[Katrien Clerx]

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   = 50; 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  = 10
nsteps   = 50


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 = 1000



From: Smith, Micholas D.<mailto:smit...@ornl.gov>
Sent: woensdag 26 februari 2020 14:10
To: Katrien Clerx<mailto:katrien.cl...@student.kuleuven.be>; 
gmx-us...@gromacs.org<mailto:gmx-us...@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 o

Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

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-boun...@maillist.sys.kth.se 
 on behalf of Katrien Clerx 

Sent: Wednesday, February 26, 2020 7:52 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis

Yes I used double precision for everything.



-Katrien







From: Smith, Micholas D.<mailto:smit...@ornl.gov>
Sent: woensdag 26 februari 2020 13:39
To: gmx-us...@gromacs.org<mailto:gmx-us...@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-boun...@maillist.sys.kth.se 
 on behalf of Katrien Clerx 

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@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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Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

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-boun...@maillist.sys.kth.se 
 on behalf of Katrien Clerx 

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@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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Re: [gmx-users] Normal mode analysis

[Katrien Clerx]

Yes I used double precision for everything.



-Katrien







From: Smith, Micholas D.<mailto:smit...@ornl.gov>
Sent: woensdag 26 februari 2020 13:39
To: gmx-us...@gromacs.org<mailto:gmx-us...@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-boun...@maillist.sys.kth.se 
 on behalf of Katrien Clerx 

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@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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[gmx-users] Normal mode analysis

[Katrien Clerx]

?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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Re: [gmx-users] Normal Mode Analysis

[Adip Jhaveri]

Thank you for the response.
But how will the system be affected when I remove the constraints? I am
trying to get a measure of the entropy by the normal mode analysis, so will
removing the constraints lead to an incorrect estimation?

Regards,
Adip

On Thu, Oct 17, 2019 at 4:06 AM David van der Spoel 
wrote:

> Den 2019-10-16 kl. 23:31, skrev Adip Jhaveri:
> > Hello All,
> > I am simulating two proteins in solution and would like to perform Normal
> > Mode Analysis on trajectory snapshots.
> >
> > I take one particular frame in the trajectory and minimize it, followed
> by
> > mdrun for normal mode analysis. However I am getting constraint errors in
> > each of the two steps -
> > 1) In minimization it is recommended to use 'cg' method but this does not
> > work and it throws an error due to the constraints present in the system.
> > 2) I tried using the 'steep' method for minimization but then, during the
> > normal mode mdrun, it is giving an error on constraints. How do I solve
> > this problem? Do I completely remove the constraints and then perform
> 'cg'
> > minimization and 'nm' mdrun?
> Yes.
>
> >
> > Regards,
> > Adip
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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>
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Re: [gmx-users] Normal Mode Analysis

[David van der Spoel]

Den 2019-10-16 kl. 23:31, skrev Adip Jhaveri:

Hello All,
I am simulating two proteins in solution and would like to perform Normal
Mode Analysis on trajectory snapshots.

I take one particular frame in the trajectory and minimize it, followed by
mdrun for normal mode analysis. However I am getting constraint errors in
each of the two steps -
1) In minimization it is recommended to use 'cg' method but this does not
work and it throws an error due to the constraints present in the system.
2) I tried using the 'steep' method for minimization but then, during the
normal mode mdrun, it is giving an error on constraints. How do I solve
this problem? Do I completely remove the constraints and then perform 'cg'
minimization and 'nm' mdrun?

Yes.



Regards,
Adip




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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[gmx-users] Normal Mode Analysis

[Adip Jhaveri]

Hello All,
I am simulating two proteins in solution and would like to perform Normal
Mode Analysis on trajectory snapshots.

I take one particular frame in the trajectory and minimize it, followed by
mdrun for normal mode analysis. However I am getting constraint errors in
each of the two steps -
1) In minimization it is recommended to use 'cg' method but this does not
work and it throws an error due to the constraints present in the system.
2) I tried using the 'steep' method for minimization but then, during the
normal mode mdrun, it is giving an error on constraints. How do I solve
this problem? Do I completely remove the constraints and then perform 'cg'
minimization and 'nm' mdrun?

Regards,
Adip
-- 
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Re: [gmx-users] Normal-mode analysis in Gromacs

[Kevin C Chan]

Thank you David for your reply. In fact, I have already been using the
double precision version of Gromacs.

I will greatly appreciate it if other questions could also be covered.

Thanks,
Kevin


Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:
> >* Dear Users, *> >* I have encountered several questions when I try to
> perform NMA on a protein *>* structure from an equilibrated MD
> simulation. I were basically referred to *>* the gromacs manual ( *>*
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
> ) and
> some *>* threads in the mailing list. *> >* First, Gromacs (and in some
> literature) suggest to have L-BFGS energy *>* minimization (sometimes
> after steep and cg calculations) of the structure *>* before NMA and
> L-BFGS generally requires shifted/switched interactions. *>* However, for
> vdW the option should have been changed by introducing the *>*
> vdw-modifier and l-bfgs seems to still recognize it as cutoff. *> >*
> Second, for electrostatics, the option has been improved by *>*
> Reaction-field-zero but is it still suitable for NMA calculation? *> >*
> Third, I have achieved a maximum force of 9.78750e-01 using cg and still *
> >* got the warning: "The force is probably not small enough to ensure
> that you *>* are at a minimum." Usually how stable do we have to achieve
> in order to *>* avoid the warning? *> >* Thanks in advance for any
> experience shared. *You need to compile gromacs in double precision to
> get to low forces. > >* Kevin *>* OSU Pharmacy *> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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Re: [gmx-users] Normal-mode analysis in Gromacs

[David van der Spoel]

Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:

Dear Users,

I have encountered several questions when I try to perform NMA on a protein
structure from an equilibrated MD simulation. I were basically referred to
the gromacs manual (
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis) and some
threads in the mailing list.

First, Gromacs (and in some literature) suggest to have L-BFGS energy
minimization (sometimes after steep and cg calculations) of the structure
before NMA and L-BFGS generally requires shifted/switched interactions.
However, for vdW the option should have been changed by introducing the
vdw-modifier and l-bfgs seems to still recognize it as cutoff.

Second, for electrostatics, the option has been improved by
Reaction-field-zero but is it still suitable for NMA calculation?

Third, I have achieved a maximum force of 9.78750e-01 using cg and still
got the warning: "The force is probably not small enough to ensure that you
are at a minimum." Usually how stable do we have to achieve in order to
avoid the warning?

Thanks in advance for any experience shared.

You need to compile gromacs in double precision to get to low forces.



Kevin
OSU Pharmacy




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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[gmx-users] Normal mode analysis problem

[jhon espinosa]

Hi all


I am running a normal mode analysis on a system with 1.05 million atoms without 
solvent.

I performed extensive double precision energy minimization using conjugate 
gradient (more than

14 days using 1024 processor). and my final values are:

Potential Energy  = -8.54191598792831e+06
Maximum force =  2.40720622582240e+01 on atom 738910
Norm of force =  3.52791700889658e-02

When I want to start the NMA I do:

aprun -n 1 grompp_mpi_d -f nma.mdp -c vault.EMCG.gro -p vault.top -o 
vault.nma1_d.tpr -t vault.EMCG.trr  -maxwarn -1

aprun -n 1024 mdrun_mpi_d -deffnm vault.nma1_d

And after a couple of hour I get and error :

Using compressed symmetric sparse Hessian format.
Allocating Hessian memory...

starting normal mode calculation 'GRoups of Organic Molecules in ACtion for 
Science in water'
2114424 steps.

Maximum force: 4.32366e+03
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.

[NID 00116] 2016-09-19 04:25:18 Apid 6882392: initiated application termination
[NID 00116] 2016-09-19 04:25:20 Apid 6882392: OOM killer terminated this 
process.

Any suggestions ???

Thanks

Michael


the  nma.mdp is:

; RUN CONTROL PARAMETERS
integrator   = nm
t-init   = 000
dt   = 0.001
nsteps   = 1

; OUTPUT CONTROL OPTIONS
nstxout  = 1000
nstvout  = 0
nstfout  = 0
nstlog   = 1
nstenergy= 1
nstxtcout= 5

; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme= group
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Switch
rcoulomb = 1.0
rcoulomb_switch  = 0.8
epsilon_rf   = 1
vdw-type = Switch
rvdw = 1.0
rvdw_switch  = 0.8

; Temperature coupling
tcoupl   = V-rescale
tc-grps  = system
tau_t= 0.5
ref_t= 310



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[gmx-users] Normal Mode Analysis failing with no error message

[jhon espinosa]

Hi all


I am trying to do a Normal Mode Analysis on a protein assembly with 1.05 
million atoms

without solvent or ions. I ma trying to do so using Gromacs 5.0.4 double 
precision

using 1024 processor and up to 256 GB of RAM, but it always fails.

I do not get any error message from Gromacs in just finished.

The last lines of my error log file are:


starting normal mode calculation 'GRoups of Organic Molecules in ACtion for 
Science in water'
2114424 steps.

Maximum force: 1.59067e+03
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.

[NID 00841] 2016-08-30 16:36:59 Apid 6732636: initiated application termination
[NID 00841] 2016-08-30 16:37:01 Apid 6732636: OOM killer terminated this 
process.

Any suggestion

Michael

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[gmx-users] Normal mode analysis after equilibration

[Mario Fernández Pendás]

Dear All,

I am running simulations of a toxin placed in the middle of a bilayer. It
is known from the experiments that the equilibrium point of the toxin is in
one of the surfaces of the membrane.
I run MD with v-rescale a number of time-steps big enough to get the system
equilibrated with the toxin in the proper place.

At this stage, if I try to construct the Hessian matrix aiming to get its
eigenvalues without any energy minimization, it is likely that such
eigenvalues will be negative, isn't it? Even considering smaller time-steps
or tolerance?
By now, all my experiments confirm this trend so my question is to confirm
that I am not missing something.

Thank you very much.

Best,
Mario
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Re: [gmx-users] Normal mode analysis after equilibration

[David van der Spoel]

On 14/01/16 18:23, Mario Fernández Pendás wrote:

Dear All,

I am running simulations of a toxin placed in the middle of a bilayer. It
is known from the experiments that the equilibrium point of the toxin is in
one of the surfaces of the membrane.

What is an "equilibrium point"?


I run MD with v-rescale a number of time-steps big enough to get the system
equilibrated with the toxin in the proper place.

At this stage, if I try to construct the Hessian matrix aiming to get its
eigenvalues without any energy minimization, it is likely that such
eigenvalues will be negative, isn't it? Even considering smaller time-steps
or tolerance?

Yes you are bound to get negative eigenvalues.

Why would you want to do NM of part of a complex system anyway? You will 
suddenly throw away all the correlations with the membrane and solvent.


In my opinion normal mode analysis virtually only makes sense for 
isolated systems in the gas-phase



By now, all my experiments confirm this trend so my question is to confirm
that I am not missing something.

Thank you very much.

Best,
Mario




--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Normal mode analysis after equilibration

[Mario Fernández Pendás]

Dear David,

Thank you very much for your answer.

2016-01-14 20:20 GMT+01:00 David van der Spoel :

> On 14/01/16 18:23, Mario Fernández Pendás wrote:
>
>> Dear All,
>>
>> I am running simulations of a toxin placed in the middle of a bilayer. It
>> is known from the experiments that the equilibrium point of the toxin is
>> in
>> one of the surfaces of the membrane.
>>
> What is an "equilibrium point"?
>

I mean the position where the toxin tends to move.

I run MD with v-rescale a number of time-steps big enough to get the system
>> equilibrated with the toxin in the proper place.
>>
>> At this stage, if I try to construct the Hessian matrix aiming to get its
>> eigenvalues without any energy minimization, it is likely that such
>> eigenvalues will be negative, isn't it? Even considering smaller
>> time-steps
>> or tolerance?
>>
> Yes you are bound to get negative eigenvalues.
>
> Why would you want to do NM of part of a complex system anyway? You will
> suddenly throw away all the correlations with the membrane and solvent.
>
> In my opinion normal mode analysis virtually only makes sense for isolated
> systems in the gas-phase
>
> My intention was to try to observe how the frequencies of the different
modes change after the simulation and how different are them with respect
to the ones associated to the harmonic bonds of the system in equilibrium.
That is why I started to consider studying the eigenvalues of the Hessian.

Thank you very much.
Cheers,
Mario
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Re: [gmx-users] Normal Mode Analysis

[Vitaly V. Chaban]

Perhaps, trjconv -- to delete all you do not need?







On Wed, Oct 14, 2015 at 2:49 PM, Dan Sponseller  wrote:

> Hello.
>
> I am trying to do a Normal Mode Analysis of a polymer in water. I am
> running my minimization right now with -DFLEXIBLE defined.
>
> How do I exclude the water from the analysis. I only want the analysis
> done on the polymer.
>
> Dan Sponseller
> PhD student, George Mason University
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[gmx-users] Normal Mode Analysis

[Dan Sponseller]

Hello.

I am trying to do a Normal Mode Analysis of a polymer in water. I am running my 
minimization right now with -DFLEXIBLE defined.

How do I exclude the water from the analysis. I only want the analysis done on 
the polymer.

Dan Sponseller
PhD student, George Mason University
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[gmx-users] normal mode analysis and system size ...

[Michael Brunsteiner]

hi ,
I've been trying to perform a nromal mode analysis using (after a thorough 
energy minimization of my system)

prompt mdrun_d -v -s nm.tpr  -o nm.trr -mtx nm.mtx[...]
Maximum force: 8.56366e+00
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.Finished step 9060 out of 9060
Writing Hessian...

i ignored the warning hoping to get a away with that ... then:
prompt gmx nmeig -f nm.mtx -s nm.tpr -v nmeig.trr
[...]
Reading double precision matrix generated by Gromacs VERSION 5.0.4
Full matrix storage format, nrow=27180, ncols=27180
Diagonalizing to find vectors 1 through 50...

and at this point it has been working for something like three days now and 
still going ...my system (a sample of a small organic molecule glass)  has 
about 1 atoms(including protons) ... can anybody give me an estimate of 
what kind of system sizeis feasible for this kind of calculation? or could it 
be that gmx nmeig gets stuck (withoutwarning) when it encounters negative 
eigenvalues?

thanks,michael



===Why be happy when you could be normal?
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Re: [gmx-users] Normal mode analysis

[Leandro Bortot]

Hi Rahul,

 Did you make the vacuum minimization with a double-precision version
of gromacs using the L-BFGS algorithm? From the protocol you described it
seems you didn't do it..
 What was the maximum force after the minimization? (check the .log
file)

I hope it helps,
Leandro.



On Sat, Mar 28, 2015 at 7:26 AM, rahul dhakne rahuldhakn...@gmail.com
wrote:

 Dear all Gromacs user,

I am trying to perform the Normal Mode Analysis protein-DNA complex
 in vacuum. As the complex is highly negative charge (-163)I performed
 the energy minimization of complex in water (to neutralize the
 complex). After I get the completely minimized complex, again I have
 done energy minimization of complex (in vacuum) for just one step to
 get the .trr input file for the Normal mode analysis. As I have to
 perform the normal mode analysis in vacuum I did that. But due to
 highly negative charge it got stuck in hessian matrix calculation.
 Even though it calculate the matrix I got negative eigenvalues after
 diagonalizing the matrix.

 I also tried with complete energy minimization in vacuum and proceed
 for normal mode calculation, but again stuck with the same problem
 i.e. high negative charge (-163)

 How can I neutralize the system??

 or there is any way to do that or probably I am doing something unusual??


 Any suggestions will be very welcomed.

 Thanking you in advance!

 -
 Rahul
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[gmx-users] Normal mode analysis

[rahul dhakne]

Dear all Gromacs user,

   I am trying to perform the Normal Mode Analysis protein-DNA complex
in vacuum. As the complex is highly negative charge (-163)I performed
the energy minimization of complex in water (to neutralize the
complex). After I get the completely minimized complex, again I have
done energy minimization of complex (in vacuum) for just one step to
get the .trr input file for the Normal mode analysis. As I have to
perform the normal mode analysis in vacuum I did that. But due to
highly negative charge it got stuck in hessian matrix calculation.
Even though it calculate the matrix I got negative eigenvalues after
diagonalizing the matrix.

I also tried with complete energy minimization in vacuum and proceed
for normal mode calculation, but again stuck with the same problem
i.e. high negative charge (-163)

How can I neutralize the system??

or there is any way to do that or probably I am doing something unusual??


Any suggestions will be very welcomed.

Thanking you in advance!

-
Rahul
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Re: [gmx-users] Normal mode analysis error

[Justin Lemkul]

On 3/17/15 8:16 AM, rahul dhakne wrote:

Dear all,


I am trying to perform the Normal Mode Analysis protein in water.
Here is the .mdp file I am using:


integrator  = nm; time step
nsteps  =  10  ; number of steps
nstlist =  10; update pairlist
ns_type =  grid ; pairlist methodi
coulombtype =  PME
nstxtcout   =  1.0
cutoff-scheme   = Verlet
rcoulomb=  1.0
rvdw=  1.0
ewald_rtol  =  1.0
rlist   =  1.0  ; cut-off for ns
constraints = none
define  = -DWHATEVER



And I get the error message:

Fatal error:
Constraints present with Normal Mode Analysis, this combination is not
supported.



It's probably from the water, which have SETTLE constraints.  In this case you 
need -DFLEXIBLE or however the water topology might disable SETTLE.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Normal mode analysis error

[rahul dhakne]

Dear all,


I am trying to perform the Normal Mode Analysis protein in water.
Here is the .mdp file I am using:


integrator  = nm; time step
nsteps  =  10  ; number of steps
nstlist =  10; update pairlist
ns_type =  grid ; pairlist methodi
coulombtype =  PME
nstxtcout   =  1.0
cutoff-scheme   = Verlet
rcoulomb=  1.0
rvdw=  1.0
ewald_rtol  =  1.0
rlist   =  1.0  ; cut-off for ns
constraints = none
define  = -DWHATEVER



And I get the error message:

Fatal error:
Constraints present with Normal Mode Analysis, this combination is not
supported.


Any suggestions will be very welcomed.

 Thanking you in advance!


-- 
-
Rahul
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[gmx-users] Normal Mode Analysis

[xy21hb]

Dear all,


I wonder if there is anywhere I can know the details of mdp files used for 
normal mode analysis.
I understand from the maunal that it needs steepest descent, conjugate 
gradient, l-bfgs, nm in md options consecutively,
but I am not sure about other parameters set in these different stages.


Many thanks,


OAY 
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[gmx-users] normal mode analysis - regd

[ramesh cheerla]

Dear  Gromacs users,

  I am performing normal mode analysis (NMA) for a crystal, but
in the vibrational spectrum that obtained from NMA,  there are no low
frequency lattice modes ( i.e., no peaks in spectrum below 50 cm-1).  But
the spectrum that have obtained from velocity auto correlation function
(VACF) contains these low frequency peaks.
Here my doubt is why NMA was unable to capture  these low frequency
peaks(modes) ?

Can anybody please help me in this regard.

Thank you in advance.



Best,
Ramesh
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Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

[Mark Abraham]

Why are you using PME-switch? Without explicitly choosing a switch?

Mark


On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 mcfc1...@gmail.com wrote:

 Hello Everyone，

 I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot
 but
 find little useful.
 My Gromacs was installed in a Linux cluster.

 Follows is my steps to do normal mode analysis:

 • pdb2gmx -ignh -ff  forcefield  -f protein.pdb -o mut.gro -p topol.top
 • editconf -f mut.gro -o box.gro -d 1.5
 • grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
 • mdrun -s em.tpr -deffnm em -c em.g96 -v
 • grompp -f nm.mdp -c em.g96 -o nm.tpr
   ---WARNING 1 [file nm.mdp]:
 The switching range for PME-Switch should be 5% or
 less, energy
 conservation will be good anyhow, since ewald_rtol
 =
 1e-05

 I have taken advises from the forum that I should not genbox and should use
 cg instead steep for em in order to do Normal Mode Analysis, but now I am
 facing problem of PME-Switch.

 Does anyone have any experience on this?

 Thanks in advance.

 Kevin


 ==Attached is em.mdp and nm.mdp=
 em.mdp

 define  =  -DFLEXIBLE
 constraints =  none
 integrator  =  cg
 dt  =  0.002; ps !
 nsteps  =  400
 nstlist =  10
 ns_type =  grid
 rlist   =  1.0
 coulombtype =  PME
 rcoulomb=  1.0
 vdwtype =  cut-off
 rvdw=  1.4
 optimize_fft=  yes
 emtol   =  1000
 emstep  =  0.01

 ---
 nm.mdp
 constraints =  none
 integrator  =  nm
 dt  =  0.002; ps !
 nsteps  =  400
 nstlist =  10
 ns_type =  grid
 rlist   =  1.2
 coulombtype =  PME-Switch
 rcoulomb=  1.0
 vdwtype =  Cut-off
 rvdw=  1.4

 --
 View this message in context:
 http://gromacs.5086.x6.nabble.com/Normal-Mode-Analysis-with-Gromacs-4-6-tp5013240p5013276.html
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Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

[mcfc1301]

Hello Everyone， 

I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but
find little useful. 
My Gromacs was installed in a Linux cluster. 

Follows is my steps to do normal mode analysis: 

• pdb2gmx -ignh -ff  forcefield  -f protein.pdb -o mut.gro -p topol.top 
• editconf -f mut.gro -o box.gro -d 1.5 
• grompp -f em.mdp -c box.gro -p topol.top -o em.tpr 
• mdrun -s em.tpr -deffnm em -c em.g96 -v 
• grompp -f nm.mdp -c em.g96 -o nm.tpr 
  ---WARNING 1 [file nm.mdp]: 
The switching range for PME-Switch should be 5% or
less, energy 
conservation will be good anyhow, since ewald_rtol =
1e-05

I have taken advises from the forum that I should not genbox and should use
cg instead steep for em in order to do Normal Mode Analysis, but now I am
facing problem of PME-Switch. 

Does anyone have any experience on this? 
  
Thanks in advance. 

Kevin 


==Attached is em.mdp and nm.mdp= 
em.mdp 

define  =  -DFLEXIBLE 
constraints =  none 
integrator  =  cg 
dt  =  0.002; ps ! 
nsteps  =  400 
nstlist =  10 
ns_type =  grid 
rlist   =  1.0 
coulombtype =  PME 
rcoulomb=  1.0 
vdwtype =  cut-off 
rvdw=  1.4 
optimize_fft=  yes 
emtol   =  1000 
emstep  =  0.01 

--- 
nm.mdp
constraints =  none 
integrator  =  nm 
dt  =  0.002; ps ! 
nsteps  =  400 
nstlist =  10 
ns_type =  grid 
rlist   =  1.2 
coulombtype =  PME-Switch 
rcoulomb=  1.0 
vdwtype =  Cut-off 
rvdw=  1.4

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[gmx-users] Normal Mode Analysis

[Sathish Kumar]

Dear users,

   I am trying to do NMA

First i did energy minimization using .mdp file with conjugate gradient
method,

Next i calculated hessian matrix by using integrator = nm

Then i calculated the eigen vectors from 7 to 100 using g_nmeig

to analyze eigen vectors i use the commands

g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj
proj-ev1.xvg -extr

ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30


by visuvalizing ev1.pdb, i did not found any motion in the protein.


what is the mistake i have done?

Is it correct procedure for doing NM analysis?

How to analyze the eigen values obtained from hessian matrix?


regards
M.SathishKumar
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Re: [gmx-users] Normal Mode Analysis

[Sathish Kumar]

Is that ensemble of structures are related to each eigen vector or total
eigen vectors.

If i want to see the motion of seventh eigen vector how can i get?


On Mon, Nov 25, 2013 at 9:50 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 From g_nmeig -h:

 An ensemble of structures can be generated from the eigenvectors with
 g_nmens.

 Cheers,

 Tsjerk


 On Mon, Nov 25, 2013 at 5:05 PM, Sathish Kumar sathishk...@gmail.com
 wrote:

  Dear users,
 
 I am trying to do NMA
 
  First i did energy minimization using .mdp file with conjugate gradient
  method,
 
  Next i calculated hessian matrix by using integrator = nm
 
  Then i calculated the eigen vectors from 7 to 100 using g_nmeig
 
  to analyze eigen vectors i use the commands
 
  g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj
  proj-ev1.xvg -extr
 
  ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30
 
 
  by visuvalizing ev1.pdb, i did not found any motion in the protein.
 
 
  what is the mistake i have done?
 
  Is it correct procedure for doing NM analysis?
 
  How to analyze the eigen values obtained from hessian matrix?
 
 
  regards
  M.SathishKumar
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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 --
 Tsjerk A. Wassenaar, Ph.D.
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-- 
regards
M.SathishKumar
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Re: [gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi Sathish,

Have you tried reading the g_nmens manpage or the manual?

Cheers,

Tsjerk


On Mon, Nov 25, 2013 at 6:00 PM, Sathish Kumar sathishk...@gmail.comwrote:

 Is that ensemble of structures are related to each eigen vector or total
 eigen vectors.

 If i want to see the motion of seventh eigen vector how can i get?


 On Mon, Nov 25, 2013 at 9:50 PM, Tsjerk Wassenaar tsje...@gmail.com
 wrote:

  From g_nmeig -h:
 
  An ensemble of structures can be generated from the eigenvectors with
  g_nmens.
 
  Cheers,
 
  Tsjerk
 
 
  On Mon, Nov 25, 2013 at 5:05 PM, Sathish Kumar sathishk...@gmail.com
  wrote:
 
   Dear users,
  
  I am trying to do NMA
  
   First i did energy minimization using .mdp file with conjugate gradient
   method,
  
   Next i calculated hessian matrix by using integrator = nm
  
   Then i calculated the eigen vectors from 7 to 100 using g_nmeig
  
   to analyze eigen vectors i use the commands
  
   g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg
 -proj
   proj-ev1.xvg -extr
  
   ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30
  
  
   by visuvalizing ev1.pdb, i did not found any motion in the protein.
  
  
   what is the mistake i have done?
  
   Is it correct procedure for doing NM analysis?
  
   How to analyze the eigen values obtained from hessian matrix?
  
  
   regards
   M.SathishKumar
   --
   Gromacs Users mailing list
  
   * Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
   posting!
  
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   send a mail to gmx-users-requ...@gromacs.org.
  
 
 
 
  --
  Tsjerk A. Wassenaar, Ph.D.
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 --
 regards
 M.SathishKumar
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-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Normal Mode Analysis

[lloyd riggs]

I dont know your energy break down, if you look at frames with g_anaeig using -first and -last to set your vector number(s), and then frames set to your time units desired, it will give you something you can look at with vmd or pymol. I have noticed though after the frst 4 or so vectors, it becomes dificult to see movement, as the enrgy break down for even larger proteins starts to become close to single amino acid or very small single atom contributions to the entire energy landscape. Thus hard to spot visually, as the enrgies might be only one or two high energy hydrogen bonds, etc...



Stephan Watkins



Gesendet:Montag, 25. November 2013 um 17:05 Uhr
Von:Sathish Kumar sathishk...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:[gmx-users] Normal Mode Analysis

Dear users,

I am trying to do NMA

First i did energy minimization using .mdp file with conjugate gradient
method,

Next i calculated hessian matrix by using integrator = nm

Then i calculated the eigen vectors from 7 to 100 using g_nmeig

to analyze eigen vectors i use the commands

g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj
proj-ev1.xvg -extr

ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30


by visuvalizing ev1.pdb, i did not found any motion in the protein.


what is the mistake i have done?

Is it correct procedure for doing NM analysis?

How to analyze the eigen values obtained from hessian matrix?


regards
M.SathishKumar
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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