Re: [gmx-users] pressure coupling

[mohammad agha]

Thank you very much.

Yes, I checked NPT run and I saw the size and volume of box had been increased. 
So I increased size of box to 12.
My system consists of: 151 lipids+151 ions+16200 water and antifreezawater 
molecules

May I know your idea about this, please?

Best Regards
Sara




 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Saturday, December 17, 2011 10:22 AM
Subject: Re: [gmx-users] pressure coupling
 

On 17/12/2011 5:40 PM, mohammad agha wrote: 
Thank you very much.
>Excuse me, I did another thing, may I know is it right, Please?
>
>I did editconf before equilibration (pr.mdp) and increased my box vector from 
>11.2 to 12:
>editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12 12 12 -center 6 6 6
>and I minimized my system (out.gro) and then did equilibration
  (pr.mdp). My system gave me warning for box sizes 11.4, 11.6
  and 11.8, consequently I select 12 and pr.mdp is run without
  warning.
>Is it right?
We don't know. You've been changing your box volume but haven't said
anything about the contents. You need to look at how the box changes
over the NPT run, like I said last time. If your generated solvent
density was wrong such that you needed to add about 20% more volume,
then expect to need to equilibrate for quite a while.

Mark



>
>Best Regards
>Sara
>
>
>
>
>
>
>
>
>
>
>
>
>
> From: Mark Abraham 
>To: Discussion list for GROMACS users  
>Sent: Saturday, December 17, 2011 9:31 AM
>Subject: Re: [gmx-users] pressure coupling
> 
>
>On 17/12/2011 4:58 PM, mohammad agha wrote: 
>Dear GROMACS Users
>>
>>
>>I have a warning after doing pr.mdp as followed, I read errors in GROMACS 
>>site and checked mailing list, but my warning is only step1 and after that 
>>equilibration is run normally till end.  
>>
>>
>>
>>
>>
>>500 steps, 15.0 ps.
>>step 0
>>Step 1  Warning: pressure scaling more than 1%,
  mu: 1.04679 1.04679 1.04679
>>
>>Step 1  Warning: pressure scaling more than 1%,
  mu: 1.04679 1.04679 1.04679
>>
>>
>>
>>my pr.mdp about pressure coupling is:
>>
>>
>>pcoupl        = berendsen
>>pcoupltype    = isotropic    ; uniform scaling of
  box vectors
>>tau_p        = 4 ; time constant, in ps
>>ref_p        = 1.0     ; reference pressure, in
  bar
>>compressibility = 4.5e-5  ;isothermal
  compressibility of water, bar^-1
>>
>>
>>
>>
>>I work in Martini Coarse-Grained and my time step is 0.03 ps. I increased 
>>tau_p but my warning increased to step 1 and step 11, I think this warning 
>>since it is only in initial steps isn't important, is my idea right?
>>
>That kind of thing is normal in the very early stages of
NPT equilibration when the volume is not quite right.
mdrun is just warning you that there are some changes
going on. Use g_energy to see those. If it bothers you,
then you will want to adjust your density (i.e. number
of water molecules) before starting.
>
>Mark
>
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Re: [gmx-users] pressure coupling

[Mark Abraham]

On 17/12/2011 5:40 PM, mohammad agha wrote:

Thank you very much.
Excuse me, I did another thing, may I know is it right, Please?
I did editconf before equilibration (pr.mdp) and increased my box 
vector from 11.2 to 12:
editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12 12 12 
-center 6 6 6
and I minimized my system (out.gro) and then did equilibration 
(pr.mdp). My system gave me warning for box sizes 11.4, 11.6 and 11.8, 
consequently I select 12 and pr.mdp is run without warning.

Is it right?


We don't know. You've been changing your box volume but haven't said 
anything about the contents. You need to look at how the box changes 
over the NPT run, like I said last time. If your generated solvent 
density was wrong such that you needed to add about 20% more volume, 
then expect to need to equilibrate for quite a while.


Mark



Best Regards
Sara






*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, December 17, 2011 9:31 AM
*Subject:* Re: [gmx-users] pressure coupling

On 17/12/2011 4:58 PM, mohammad agha wrote:

Dear GROMACS Users

I have a warning after doing pr.mdp as followed, I read errors in 
GROMACS site and checked mailing list, but my warning is only step1 
and after that equilibration is run normally till end.



500 steps, 15.0 ps.
step 0
Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


my pr.mdp about pressure coupling is:

pcoupl= berendsen
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 4 ; time constant, in ps
ref_p= 1.0 ; reference pressure, in bar
compressibility = 4.5e-5  ;isothermal compressibility of water, bar^-1


I work in Martini Coarse-Grained and my time step is 0.03 ps. I 
increased tau_p but my warning increased to step 1 and step 11, I 
think this warning since it is only in initial steps isn't important, 
is my idea right?




That kind of thing is normal in the very early stages of NPT 
equilibration when the volume is not quite right. mdrun is just 
warning you that there are some changes going on. Use g_energy to see 
those. If it bothers you, then you will want to adjust your density 
(i.e. number of water molecules) before starting.


Mark

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Re: [gmx-users] pressure coupling

[mohammad agha]

Thank you very much.
Excuse me, I did another thing, may I know is it right, Please?

I did editconf before equilibration (pr.mdp) and increased my box vector from 
11.2 to 12:
editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12 12 12 -center 6 6 6
and I minimized my system (out.gro) and then did equilibration (pr.mdp). My 
system gave me warning for box sizes 11.4, 11.6 and 11.8, consequently I select 
12 and pr.mdp is run without warning.
Is it right?

Best Regards
Sara








 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Saturday, December 17, 2011 9:31 AM
Subject: Re: [gmx-users] pressure coupling
 

On 17/12/2011 4:58 PM, mohammad agha wrote: 
Dear GROMACS Users
>
>
>I have a warning after doing pr.mdp as followed, I read errors in GROMACS site 
>and checked mailing list, but my warning is only step1 and after that 
>equilibration is run normally till end.  
>
>
>
>
>
>500 steps, 15.0 ps.
>step 0
>Step 1  Warning: pressure scaling more than 1%, mu: 1.04679
  1.04679 1.04679
>
>Step 1  Warning: pressure scaling more than 1%, mu: 1.04679
  1.04679 1.04679
>
>
>
>my pr.mdp about pressure coupling is:
>
>
>pcoupl        = berendsen
>pcoupltype    = isotropic    ; uniform scaling of box vectors
>tau_p        = 4 ; time constant, in ps
>ref_p        = 1.0     ; reference pressure, in bar
>compressibility = 4.5e-5  ;isothermal compressibility of
  water, bar^-1
>
>
>
>
>I work in Martini Coarse-Grained and my time step is 0.03 ps. I increased 
>tau_p but my warning increased to step 1 and step 11, I think this warning 
>since it is only in initial steps isn't important, is my idea right?
>
That kind of thing is normal in the very early stages of NPT
equilibration when the volume is not quite right. mdrun is just
warning you that there are some changes going on. Use g_energy to
see those. If it bothers you, then you will want to adjust your
density (i.e. number of water molecules) before starting.

Mark

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Re: [gmx-users] energy_terms

[Mark Abraham]

On 17/12/2011 5:25 PM, balaji nagarajan wrote:

Dear Users !

I have used the energy group option to split the energy terms , for 
the protein and the water.


You have split the *non-bonded* terms.



It gives all the terms ,

protein-protein , water-water , water-protein .

I have a doubt ,
the distance and the angle are taken for both water and the protein ,


I don't see what distance and angle you mean.



how one can get these energy terms for protein alone.


What energy terms do you want? You have the intra-protein non-bonded 
energies above.


Mark
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[gmx-users] energy_terms

[balaji nagarajan]

Dear Users ! 

I have used the energy group option to split the energy terms , for the protein 
and the water. 

It gives all the terms , 

protein-protein , water-water , water-protein .

I have a doubt , 
the distance and the angle are taken for both water and the protein , 

how one can get these energy terms for protein alone.

thanks in advance 


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Re: [gmx-users] pressure coupling

[Mark Abraham]

On 17/12/2011 4:58 PM, mohammad agha wrote:

Dear GROMACS Users

I have a warning after doing pr.mdp as followed, I read errors in 
GROMACS site and checked mailing list, but my warning is only step1 
and after that equilibration is run normally till end.



500 steps, 15.0 ps.
step 0
Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


my pr.mdp about pressure coupling is:

pcoupl= berendsen
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 4 ; time constant, in ps
ref_p= 1.0 ; reference pressure, in bar
compressibility = 4.5e-5  ;isothermal compressibility of water, bar^-1


I work in Martini Coarse-Grained and my time step is 0.03 ps. I 
increased tau_p but my warning increased to step 1 and step 11, I 
think this warning since it is only in initial steps isn't important, 
is my idea right?




That kind of thing is normal in the very early stages of NPT 
equilibration when the volume is not quite right. mdrun is just warning 
you that there are some changes going on. Use g_energy to see those. If 
it bothers you, then you will want to adjust your density (i.e. number 
of water molecules) before starting.


Mark
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[gmx-users] pressure coupling

[mohammad agha]

Dear GROMACS Users

I have a warning after doing pr.mdp as followed, I read errors in GROMACS site 
and checked mailing list, but my warning is only step1 and after that 
equilibration is run normally till end.  



500 steps, 15.0 ps.
step 0
Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 1.04679

Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 1.04679


my pr.mdp about pressure coupling is:

pcoupl        = berendsen
pcoupltype    = isotropic    ; uniform scaling of box vectors
tau_p        = 4 ; time constant, in ps
ref_p        = 1.0     ; reference pressure, in bar
compressibility = 4.5e-5  ;isothermal compressibility of water, bar^-1


I work in Martini Coarse-Grained and my time step is 0.03 ps. I increased tau_p 
but my warning increased to step 1 and step 11, I think this warning since it 
is only in initial steps isn't important, is my idea right?

Best Regards
Sara
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[gmx-users] About plumed gromacs umbrella pulling

[vidhya sankar]

Dear jusitn Thank you for your previous reply.
  I am 
doing Umbrella sampling using plumed-gromacs. for that i have done umbrella 
pulling using gromacs only 

I have extracted the frame of reference from 120ps to 360ps . i am using these 
set of trajectories for the Umbrella sampling in plumed gromacs (interface with 
plumed)
when i do the sampling using plumed-gromacs i used gromacs  mdp files with 
option of  tinit =120  while i define all these extracted pdbs (from 120 to 
360ns) in plumed .dat file . is it  appropriate  ?  i Think when 
plumed-gromacs    do the sampling, it consider from 120 to 360 ns trajectories 
only. is it correct?. i have provided the plumed.dat and md.mdp file as below 
kindly consider and go through it  . i am expecting your valuable  reply
   PRINT W_STRIDE 100 
    S_PATH TYPE RMSD FRAMESET mdoutput  NFRAMES 24 LAMBDA 72.634290 
    Z_PATH TYPE RMSD FRAMESET mdoutput  NFRAMES 24 LAMBDA 72.634290 
    UMBRELLA CV 1 KAPPA 1000 AT 0.00
    UMBRELLA CV 2 KAPPA 1000 AT 0.00
    ENDMETA


title   = Umbrella pulling simulation 
define  = -DPOSRES_B
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 120
nsteps  = 25    ;
nstcomm = 10
; Output parameters
nstxout = 50  ; 
nstvout = 50 
nstfout = 50
nstxtcout   = 50  
nstenergy   = 50
; Bond parameters
constraint_algorithm    = lincs
constraints = all-bonds
continuation    = yes   ; continuing from NPT 
; Single-range cutoff scheme
nstlist = 5
ns_type = grid 
rlist   = 1.4
rcoulomb    = 1.4
rvdw    = 1.4
; PME electrostatics parameters
coulombtype    =  PME  
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein   Non-Protein 
tau_t   = 0.5   0.5
ref_t   = 310   310
; SIMULATED ANNEALING  
; Type of annealing for each temperature group (no/single/periodic)
;annealing    = periodic single
; Number of time points to use for specifying annealing in each group
;annealing_npoints    = 5 3
; List of times at the annealing points for each group
;annealing_time   = 0 3 6 9 12  0 2 4
; Temp. at each annealing point, for each group.
;annealing_temp  = 310 320 298 298 310  310 320 310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman 
pcoupltype  = isotropic
tau_p   = 1.0   
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no 
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
;pull    = umbrella
;pull_geometry   = distance  ; simple distance increase 
;pull_dim    = N N Y
;pull_start  = yes   ; define initial COM distance > 0
;pull_ngroups    = 1
;pull_group0 = Chain_B 
;pull_group1 = Chain_A 
;pull_rate1  = 0  ; 0.01 nm per ps = 10 nm per ns
;pull_k1 = 1000  ; kJ mol^-1 nm^-2-- 
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Re: [gmx-users] Voronoi tessellation

[Justin A. Lemkul]

Ramya Parthasarathi wrote:

Hi

I am working with phospholipid bilayers and I would like to plot the 2D 
Voronoi Tessellation , can any one tell me how to start about it.




Not with any Gromacs tool.  But these might be useful:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.21973/abstract
http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Voronoi tessellation

[Ramya Parthasarathi]

Hi 

I am working with phospholipid bilayers and I would like to plot the 2D Voronoi 
Tessellation , can any one tell me how to start about it.

Thanks.

 

 

Ramya Parthasarathi


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Re: [gmx-users] Regarding free energy calculation

[Justin A. Lemkul]

bipin singh wrote:

Hello,

I am willing to study the free energy of binding of a cation (Ca++) to
the protein and I am following the free energy tutorial
provided by Justin
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy
).
Please let me know whether the settings for this type of study would
be same as given in the tutorial for ligand-Protein
binding free energy calculation or it need some different approach:


By decoupling a Ca2+ ion, you are removing 2 charges from the system.  I don't 
know how to properly treat such a case (perhaps someone else can comment), but 
likely you'll find such topics in the literature.  A better approach may be 
umbrella sampling, but again the literature should point you to reasonable 
methodology.  I'm sure others have dealt with such questions before.


-Justin


The setting from the ligand-Protein binding free energy calculation
are given as:


 van der Waals coupling:

 sc-alpha  = 0.5 ; use soft-core for LJ (de)coupling
 sc-sigma  = 0.3
 sc-power  = 1
 couple-moltype= LIG
 couple-intramol   = no
 couple-lambda0= none; non-interacting dummy in state A
 couple-lambda1= vdw ; only vdW terms on in state B

Coulombic coupling:

 sc-alpha  = 0   ; soft-core during (dis)charging can
be unstable!
 sc-sigma  = 0
 couple-moltype= LIG
 couple-intramol   = no
 couple-lambda0= vdw ; only vdW terms in state A (the
previous state B is now A)
 couple-lambda1= vdw-q   ; all nonbonded interactions are on in state B




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] tip3p water in gromacs_4.5.4

[Tomek Wlodarski]

Hi Shahid,

Use spc216.gro file, it also works for tip3p water model.
Best!

tomek

On Fri, Dec 16, 2011 at 11:26 AM, shahid nayeem  wrote:
> Dear all
> I want to use tip3p water model for solvating my protein with genbox command
> . I couldnt find tip3p.gro file in Gromacs/share/top folder . please help me
> I am following using command
> genbox -cp protein_box.gro -cs tip3p.gro -o solv.gro -p *.top
> It says tip3p.gro not found.
> Please help.
> shahid Nayeem
>
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[gmx-users] tip3p water in gromacs_4.5.4

[shahid nayeem]

Dear all
I want to use tip3p water model for solvating my protein with genbox
command . I couldnt find tip3p.gro file in Gromacs/share/top folder .
please help me
I am following using command
genbox -cp protein_box.gro -cs tip3p.gro -o solv.gro -p *.top
It says tip3p.gro not found.
Please help.
shahid Nayeem
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Re: [gmx-users] compatible gromacs

[aiswarya pawar]

I did the openmpi installation on IBM cluster, when i try to run the md.tpr
is read but gets abort and leaves and error saying=

p4_error: interrupt SIGx:4

Anyone knows the solution to this.

Thanks,
Aiswarya

On Fri, Dec 16, 2011 at 2:28 PM, Mark Abraham wrote:

> On 16/12/2011 4:55 PM, aiswarya pawar wrote:
>
>> Hi users,
>>
>> i would like to know which version of gromacs would be compatible with
>> the cluster architecture =
>>
>> Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
>> ppc64 ppc64 ppc64 GNU/Linux
>>
>
> Any.
>
>
>
>> And which gromacs version would be compatible with the mpi version =
>> mpich-1.2.7
>>
>
> Don't know - use of MPICH is discouraged because of some historical
> problems. Knowledge that a particular version works well with modern
> version of GROMACS would be a useful addition to the installation guide.
>
> Mark
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Re: [gmx-users] compatible gromacs

[Mark Abraham]

On 16/12/2011 4:55 PM, aiswarya pawar wrote:

Hi users,

i would like to know which version of gromacs would be compatible with 
the cluster architecture =


Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 
2005 ppc64 ppc64 ppc64 GNU/Linux


Any.



And which gromacs version would be compatible with the mpi version = 
mpich-1.2.7


Don't know - use of MPICH is discouraged because of some historical 
problems. Knowledge that a particular version works well with modern 
version of GROMACS would be a useful addition to the installation guide.


Mark
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Re: [gmx-users] calculation of density for martini coarse-grained

[Tsjerk Wassenaar]

Hi Sara,

For calculation of the density you need the masses. Neither editconf
nor genbox uses real masses. They approximate the mass based on a list
of atom names and associated masses, which is quite crude and fails if
the atoms are not listed. Martini beads are not listed...
To get the density you have to look at the .edr file that is written
during the simulation.

Cheers,

Tsjerk

On Fri, Dec 16, 2011 at 7:02 AM, mohammad agha  wrote:
> Excuse me, I did all of examples in my system with different molecules (even
> water alone) and with different force fields and I took this warning for all
> of them by doing genbox command!!!
>
> WARNING: masses and atomic (Van der Waals) radii will be determined
>  based on residue and atom names. These numbers can deviate
>  from the correct mass and radius of the atom type.
>
> Is this warning for all in this command, always? If not, then why have I
> that always? My density is calculated wrong in gromacs and density is
> important for me!
> Please help me.
>
> Best Regards
> Sara
> 
> From: mohammad agha 
> To: "jalem...@vt.edu" ; Discussion list for GROMACS users
> 
> Sent: Thursday, December 15, 2011 10:28 PM
>
> Subject: Re: [gmx-users] calculation of density for martini coarse-grained
>
> Thank you very much.
>
> Best Regards
>
> Sara
>
> 
> From: Justin A. Lemkul 
> To: Discussion list for GROMACS users 
> Sent: Thursday, December 15, 2011 10:02 PM
> Subject: Re: [gmx-users] calculation of density for martini coarse-grained
>
>
>
> mohammad agha wrote:
>> Thank you very much for your reply.
>>
>> I experienced "genbox" for gromos force field for my molecules and for
>> dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same
>> warning for all them!!!
>> May I know that what should I do, Please ?
>>
>
> Probably nothing.  If you use a coordinate file as input into a number of
> tools you'll likely get the same.  As I said, it is a warning, not an error
> that needs fixing.  It is up to you, as the user, to verify that the output
> of the program is what you want it to be.  Issues related to measured
> density as you've been reporting are likely a consequence of bizarre atom
> names that Gromacs doesn't understand.  You have to (correctly) do the math
> to find what the density should be.
>
> -Justin
>
>> Best Regards
>> Sara
>> 
>> *From:* Justin A. Lemkul 
>> *To:* mohammad agha ; Discussion list for GROMACS users
>> 
>> *Sent:* Thursday, December 15, 2011 9:26 PM
>> *Subject:* Re: [gmx-users] calculation of density for martini
>> coarse-grained
>>
>>
>>
>> mohammad agha wrote:
>>  > Dear Prof.
>>  >
>>  > Thank you very much.
>>  > Excuse me, I am beginner in gromacs and my experience about warnings is
>> low, but I think my problem return to this warning:
>>  >
>>  > WARNING: masses and atomic (Van der Waals) radii will be determined
>>  >          based on residue and atom names. These numbers can deviate
>>  >          from the correct mass and radius of the atom type.
>>  >
>>
>> The warning indicates that names may give misleading values for masses and
>> van der Waals interactions.  For instance, is "CA" an alpha-carbon, or
>> calcium?  In this context, the program reporting the error doesn't know.
>> Since MARTINI uses lots of weird atom names for its structures, the program
>> is warning you that the output may be incorrect, or perhaps it may not;
>> hence why it is a warning and not an error.
>>
>> -Justin
>>
>>  > I checked mailing list but I didn't find my answer!
>>  > Please help me.
>>  >
>>  > Best Regards
>>  >
>>  > Sara
>>  >
>> 
>>  > *From:* Mark Abraham > >
>>  > *To:* Discussion list for GROMACS users > >
>>  > *Sent:* Thursday, December 15, 2011 6:31 PM
>>  > *Subject:* Re: [gmx-users] calculation of density for martini
>> coarse-grained
>>  >
>>  > On 16/12/2011 1:36 AM, mohammad agha wrote:
>>  >> Dear Prof.
>>  >>
>>  >> Thank you for your reply.
>>  >> I'm really sorry for my mistake in writing the density!! my calculated
>> density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
>>  >> In the martini_v2.0.itp file, has been written "all particle masses
>> are set to 72 amu". May I know my mistake, Please?
>>  >>
>>  >> My solvent molecules aren't named "SOL".
>>  >>
>>  >> Command lines and terminal outputs:
>>  >>
>>  >> 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
>>  >> output of terminal is:
>>  >> Output configuration contains 755 atoms in 151 residues
>>  >> Volume                :        1000 (nm^3)
>>  >> Density                :    15.8111 (g/l)
>>  >> Number of SOL molecules:      0  >
>>  > One possibility is that the Martini force field doesn't have the masses
>> set up correctly for genbox to 

Re: [gmx-users] Re: Eigenvalue values from PCA (a general question)

[Tsjerk Wassenaar]

Hi Michiel,

You're right there. The OP may have assumed that the numbers were
percentages, whereas they are the eigenvalues, which remain to be
divided by the total variance to get the cumulative fraction of
variance explained. The variance explained by the first ten pc's in
this case is approximately 32 / (trace of covariance matrix). I
naively assumed that the 30% referred to by the OP corresponded to the
fraction.

Cheers,

Tsjerk

On Fri, Dec 16, 2011 at 7:37 AM, Niesen, Michiel  wrote:
>>Hi Michiel,
>>
>>I disagree, and so does semantics. The cumulative variance of a pc is the
>>variance of it plus the sum of the preceding ones. You're talking about the
>>cumulative fraction of the total variance.
>
> You are right about the proper word usage. It seemed to me from his question, 
> the use of a % mark when discussing the variance covered by the first 10 PCs, 
> and the conclusions drawn from the value he calculated, that Vijayan meant 
> the cumulative fraction of the total variance. I should name it properly, but 
> I still believe that cumulative fraction of the total variance is the 
> property Vijayan would be interested in.
>
> Regards,
>  Michiel
>
>
>>
>>Cheers,
>>
>>Tajerk
>>
>>On Dec 16, 2011 12:07 AM, "Niesen, Michiel"  wrote:
>>
>>>Date: Thu, 15 Dec 2011 15:11:12 -0500
>>>From: "R.S.K.Vijayan" 
>>>Subject: [gmx-users] Eigenvalue values from PCA (a general question)
>>>To: gmx-users@gromacs.org
>>>Message-ID:
>>>       
>>>Content-Type: text/plain; charset="iso-8859-1"
>>
>>> >Hi all > >I have a query about the eigenvalue values obtained from
>>g_covar and >g_anaeig > >I pe...
>>
>>>What i infer from this is that the cumulative variance experienced by the
>>>top 10 PC is hardly ~ ...
>>The cumulative variance described by a set of PCs is not the sum of their
>>eigenvalues. You have to take the sum of the first x eigenvalues as a
>>percentage of the sum of all eigenvalues to get the cumulative variance.
>>
>>>a) does this imply inadequate sampling by MD or a limited conformational
>>>change happening in the...
>>
>>>b) is it wise to consider the Nucleic acid during essential dynamics or
>>>should it be discared and ...
>>
>>>Thanking you in advance for your suggestions. My apologies since it sound
>>>to be a very general que...
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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