Re: [gmx-users] density profile

[Justin Lemkul]

On 3/31/13 1:12 PM, Elisabeth wrote:

Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.

Here are the steps:

1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and cpt file as input for the next step
2- I extended the box in Z to more than twice the initial box size and
issued the following:

grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr
mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v

My questions are:

1) Can I get the proper solvent-air interface to obtain density profile by
extending the Z direction (last line of the gro file obtained from NPT at
each pressure)? Is that what yo mean by " then build a new unit cell and
run under NVT" ?


That's one approach.  It's not NVT if you're using pressure coupling, though.  I 
would also be careful about using the term "air" here - if it's empty space, 
it's actually vacuum.



2) Is the semi isotropic option with 0 compressibility in Z is appropriate
to keep the pressure fixed? (as shown below in mdp settings)?


That should work.  As long as the dimension along which you need the density 
profile is invariant, you should be able to circumvent any issues.


-Justin


3) If the answer to q 2 is negative, whats is appropriate way to shift from
NPt to NVT run. Do I have to use the equilibrated density from NPT runs and
edit the last line of gro from -c flag of NPT.gro to obtain the correct
density? The reason I am asking is that since P fluctuations are huge I am
not sure if the the density of box from last frame of -c NPT.gro output is
the correct density...

Please advise on the above queries..Thanks a lot





Below is the md.mdp contents:

pbc =  xyz


integrator  =  md

dt  =  0.001

nsteps  =  2000

nstcomm =  100



;   Output control

nstenergy   =  100

nstxout =  100;1

  nstvout =  0

nstfout =  0

nstlog  =  1000

nstxtcout   =  1000

;   Neighbor searching

nstlist =  10

ns_type =  grid

;   Electrostatics/VdW

coulombtype =  Shift

vdw-type=  Shift

rcoulomb-switch =  1

rvdw-switch =  1 ;0.9

;   Cut-offs

rlist   =  1.35

rcoulomb=  1.1   ;1.1

rvdw=  1.1


Tcoupl  =  v-rescale

tc-grps =  System

tau_t   =  0.1

ref_t   =  425

*   *

*Pcoupl  =  berendsen*

*Pcoupltype  =  semiisotropic *

*tau_p   =  1  0.5*

*compressibility =  3.5e-5  0*

*ref_p   =  50   ** *



gen_vel =  no

gen_temp=  500.0

gen_seed=  173529



constraints = none

constraint-algorithm = lincs


On 31 March 2013 12:47, Justin Lemkul  wrote:




On 3/31/13 12:27 PM, Elisabeth wrote:


Thank Justin. I am interested in the density profile at the solvent-air
interface. I wanted to see how density changes with position at different
pressures...I have the equilibrated boxes at several pressures obtained
from NPT but I am not sure whether running g_density on the current
simulations cells provides the profile I am after. Do you have any clue
whether or not the cell has to be extended in one direction to obtain the
density profile?



If you're trying to produce an air-water interface, then indeed you will
need some model for air within the unit cell, but there are several
practical problems with that.  The first is that g_density does not deal
well with changing box vectors, and the density profiles it produces under
an NPT ensemble are incorrect (outstanding bug that needs to be fixed,
IIRC).  The second is that if you run a simulation under NPT with void
space, the unit cell will just compress down until there is no empty space.
  Probably the best solution would be to equilibrate under NPT at the
desired conditions, then build a new unit cell and run under NVT.  Using
NVT will circumvent both problems, and if the proper pressure, density, etc
have already been achieved, then you've got what you're after.


-Justin

--
==**==

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

==**==
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Re: [gmx-users] density profile

[Elisabeth]

Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.

Here are the steps:

1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and cpt file as input for the next step
2- I extended the box in Z to more than twice the initial box size and
issued the following:

grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr
mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v

My questions are:

1) Can I get the proper solvent-air interface to obtain density profile by
extending the Z direction (last line of the gro file obtained from NPT at
each pressure)? Is that what yo mean by " then build a new unit cell and
run under NVT" ?
2) Is the semi isotropic option with 0 compressibility in Z is appropriate
to keep the pressure fixed? (as shown below in mdp settings)?
3) If the answer to q 2 is negative, whats is appropriate way to shift from
NPt to NVT run. Do I have to use the equilibrated density from NPT runs and
edit the last line of gro from -c flag of NPT.gro to obtain the correct
density? The reason I am asking is that since P fluctuations are huge I am
not sure if the the density of box from last frame of -c NPT.gro output is
the correct density...

Please advise on the above queries..Thanks a lot





Below is the md.mdp contents:

pbc =  xyz


integrator  =  md

dt  =  0.001

nsteps  =  2000

nstcomm =  100



;   Output control

nstenergy   =  100

nstxout =  100;1

 nstvout =  0

nstfout =  0

nstlog  =  1000

nstxtcout   =  1000

;   Neighbor searching

nstlist =  10

ns_type =  grid

;   Electrostatics/VdW

coulombtype =  Shift

vdw-type=  Shift

rcoulomb-switch =  1

rvdw-switch =  1 ;0.9

;   Cut-offs

rlist   =  1.35

rcoulomb=  1.1   ;1.1

rvdw=  1.1


Tcoupl  =  v-rescale

tc-grps =  System

tau_t   =  0.1

ref_t   =  425

*   *

*Pcoupl  =  berendsen*

*Pcoupltype  =  semiisotropic *

*tau_p   =  1  0.5*

*compressibility =  3.5e-5  0*

*ref_p   =  50   ** *



gen_vel =  no

gen_temp=  500.0

gen_seed=  173529



constraints = none

constraint-algorithm = lincs


On 31 March 2013 12:47, Justin Lemkul  wrote:

>
>
> On 3/31/13 12:27 PM, Elisabeth wrote:
>
>> Thank Justin. I am interested in the density profile at the solvent-air
>> interface. I wanted to see how density changes with position at different
>> pressures...I have the equilibrated boxes at several pressures obtained
>> from NPT but I am not sure whether running g_density on the current
>> simulations cells provides the profile I am after. Do you have any clue
>> whether or not the cell has to be extended in one direction to obtain the
>> density profile?
>>
>>
> If you're trying to produce an air-water interface, then indeed you will
> need some model for air within the unit cell, but there are several
> practical problems with that.  The first is that g_density does not deal
> well with changing box vectors, and the density profiles it produces under
> an NPT ensemble are incorrect (outstanding bug that needs to be fixed,
> IIRC).  The second is that if you run a simulation under NPT with void
> space, the unit cell will just compress down until there is no empty space.
>  Probably the best solution would be to equilibrate under NPT at the
> desired conditions, then build a new unit cell and run under NVT.  Using
> NVT will circumvent both problems, and if the proper pressure, density, etc
> have already been achieved, then you've got what you're after.
>
>
> -Justin
>
> --
> ==**==
>
> 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
>
> ==**==
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] density profile

[Justin Lemkul]

On 3/31/13 12:27 PM, Elisabeth wrote:

Thank Justin. I am interested in the density profile at the solvent-air
interface. I wanted to see how density changes with position at different
pressures...I have the equilibrated boxes at several pressures obtained
from NPT but I am not sure whether running g_density on the current
simulations cells provides the profile I am after. Do you have any clue
whether or not the cell has to be extended in one direction to obtain the
density profile?



If you're trying to produce an air-water interface, then indeed you will need 
some model for air within the unit cell, but there are several practical 
problems with that.  The first is that g_density does not deal well with 
changing box vectors, and the density profiles it produces under an NPT ensemble 
are incorrect (outstanding bug that needs to be fixed, IIRC).  The second is 
that if you run a simulation under NPT with void space, the unit cell will just 
compress down until there is no empty space.  Probably the best solution would 
be to equilibrate under NPT at the desired conditions, then build a new unit 
cell and run under NVT.  Using NVT will circumvent both problems, and if the 
proper pressure, density, etc have already been achieved, then you've got what 
you're after.


-Justin

--


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


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Re: [gmx-users] density profile

[Elisabeth]

Thank Justin. I am interested in the density profile at the solvent-air
interface. I wanted to see how density changes with position at different
pressures...I have the equilibrated boxes at several pressures obtained
from NPT but I am not sure whether running g_density on the current
simulations cells provides the profile I am after. Do you have any clue
whether or not the cell has to be extended in one direction to obtain the
density profile?

Thanks!

On 31 March 2013 12:21, Justin Lemkul  wrote:

>
>
> On 3/31/13 11:41 AM, Elisabeth wrote:
>
>> Dear all,
>>
>> In order to get density profile of a pure system the box has to get
>> extended in one drection (e.g Z) as we do for surface tension calculations
>> or density profile
>> can be also obtained from the usual box filled up with the molecules
>> without need for empty space in Z
>>
>> Thanks for any comments and advise in advance :)
>>
>
> The density of the system is written to the .edr file.  There is no need
> (or use) for a density profile if the system is homogeneous.
>
> -Justin
>
> --
> ==**==
>
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] density profile

[Justin Lemkul]

On 3/31/13 11:41 AM, Elisabeth wrote:

Dear all,

In order to get density profile of a pure system the box has to get
extended in one drection (e.g Z) as we do for surface tension calculations
or density profile
can be also obtained from the usual box filled up with the molecules
without need for empty space in Z

Thanks for any comments and advise in advance :)


The density of the system is written to the .edr file.  There is no need (or 
use) for a density profile if the system is homogeneous.


-Justin

--


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


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[gmx-users] density profile

[Elisabeth]

Dear all,

In order to get density profile of a pure system the box has to get
extended in one drection (e.g Z) as we do for surface tension calculations
or density profile
can be also obtained from the usual box filled up with the molecules
without need for empty space in Z

Thanks for any comments and advise in advance :)
Best
E.
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Re: [gmx-users] Density measurment

[Justin Lemkul]

On 10/3/12 12:22 AM, rama david wrote:

Thank you Justin for your reply ,

I tried g_density again after your reply. But I found that
it give density with respect to box dimension and not to time.



I suggested before that you could perhaps advantageously using the -b and -e 
flags to achieve something similar.  You cannot get density over time per region 
of the box automatically.  That would be some sort of 3-D graph since there are 
two quantities effectively being analyzed.



g_densmap have xpm output and no the xvg  ( I need density or no of water
molecule present in between two peptides  with respect to the time )..



The colorized plot from g_densmap can tell you quite a lot, in my opinion.

What about g_rdf?  Integrating an RDF plot will tell you how many solute 
molecules are present in a particular region of space.  Otherwise, you can also 
use g_select to determine how many water molecules are located between your 
peptides using simple geometric criteria.  Look for examples in the archive; 
people have done this before.


-Justin

--


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


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Re: [gmx-users] Density measurment

[rama david]

Thank you Justin for your reply ,

I tried g_density again after your reply. But I found that
it give density with respect to box dimension and not to time.

g_densmap have xpm output and no the xvg  ( I need density or no of water
molecule present in between two peptides  with respect to the time )..


Please, would you tell me another way to solve these problem..??

Thank you in advance

Have a nice day.
Rama David




On Tue, Oct 2, 2012 at 8:28 PM, Justin Lemkul  wrote:

>
>
> On 10/2/12 7:07 AM, rama david wrote:
>
>> Hi Gromacs Users,
>>
>>   I did simulation of two random coil peptides for 100ns.
>>   after 70 ns these peptide get converted to anti parallel beta sheet
>> structure.
>>   I am interested to see the water density in between these peptideswith
>> respect to time change
>> and also the no of water molecule between the peptide with respect to
>> time.
>>   And at the same time the distance between the peptide..
>> I need these information in xvg graph.
>>
>> I found out the distance between peptide by g_mindist
>>   but I not found the appropriate way to calculate density of water with
>> respect to time
>> between two peptides..
>>
>> I used g_density but it not gave me the information as per my need.
>>
>>
> There are a variety of options in g_density that might work, like changing
> the direction along which the box is sliced, the interval of time examined,
> etc.  I can envision this working quite well.  g_densmap can do similar
> functions, and g_rdf can probably provide you with some useful information
> as well.
>
> -Justin
>
> --
> ==**==
>
> 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
>
> ==**==
> --
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Re: [gmx-users] Density measurment

[Justin Lemkul]

On 10/2/12 7:07 AM, rama david wrote:

Hi Gromacs Users,

  I did simulation of two random coil peptides for 100ns.
  after 70 ns these peptide get converted to anti parallel beta sheet
structure.
  I am interested to see the water density in between these peptideswith
respect to time change
and also the no of water molecule between the peptide with respect to time.
  And at the same time the distance between the peptide..
I need these information in xvg graph.

I found out the distance between peptide by g_mindist
  but I not found the appropriate way to calculate density of water with
respect to time
between two peptides..

I used g_density but it not gave me the information as per my need.



There are a variety of options in g_density that might work, like changing the 
direction along which the box is sliced, the interval of time examined, etc.  I 
can envision this working quite well.  g_densmap can do similar functions, and 
g_rdf can probably provide you with some useful information as well.


-Justin

--


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


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Re: [gmx-users] density map in 3 Dimension

[Justin A. Lemkul]

jagannath mondal wrote:

Dear gromacs-users,
 I thought of sending this query again as I did not get any response in 
my last email.
  I was wondering whether there is any way to calculate the 3D density 
map of a particular selection of protein-water system ( say the water 
near the protein backbone) in gromacs.
I guess g_densmap provides a 2D map of the density. But I was looking 
for 3D map of density. I presume it might have to do with calculating 
volume of a space. But, I am not sure how to do it in gromacs.

Any help will be appreciated.



Two approaches come to mind:

1. Run g_densmap in all directions (invoking the -aver flag to change the 
dimension over which averaging is done), then somehow post-processing the output 
from the .xpm files into something meaningful.  That will involve a lot of 
scripting to parse out values from the .xpm files (which are translated from the 
various letters of the color scheme) and then assembling some sort of meaningful 
format for the output.  Doesn't sound to me like a trivial task, but perhaps it 
could be done.


2. Use g_select to define dynamic indices for water molecules that fit some 
geometric criterion, then feed these index groups into the individual frames of 
your trajectory (analyzed separately, since the index groups need not be of the 
same size), and again assemble some type of meaningful output from the 
probabilities or densities in (x,y,z) space.


I've never tried either of these nor do I have anything more specific to 
recommend, just the general workflow of thinking out loud ;)


-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] density map in 3 Dimension

[jagannath mondal]

Dear gromacs-users,
 I thought of sending this query again as I did not get any response in my last 
email.
  I was wondering whether there is any way to calculate the 3D density map of a 
particular selection of protein-water system ( say the water near the protein 
backbone) in gromacs.
I guess g_densmap provides a 2D map of the density. But I was looking for 3D 
map of density. I presume it might have to do with calculating volume of a 
space. But, I am not sure how to do it in gromacs.
Any help will be appreciated.

Jagannath-- 
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[gmx-users] density of confined water

[Sanku M]

Hi,
  I would like to know if there is a way in gromacs to calculate the 
time-averaged density of solvent which is confined between two objects , say, 
two plates or another example will be water confined between ligand and 
binding-pocket.
I was thinking about two ways for going about this but in both cases there are 
some issues:
1. I found there is a tool g_densmap but it gives a 2D density map. But, in 
this case, I guess, 3D map would have been necessary.

 2. Also, I found trjorder with -nshell option can calculate number of waters 
within a distance (with -r option) . But, in this case, I need to know volume 
of the confined space as well. I am not sure gromacs can calculate the volume 
of the confined space.

Any help or suggestion of  any other suitable  methods will be highly 
appreciated.

Sanku
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Re: [gmx-users] density

[mohammad agha]

Thanks Prof. Warren




 From: Dallas Warren 
To: Discussion list for GROMACS users  
Sent: Tuesday, November 22, 2011 12:23 AM
Subject: RE: [gmx-users] density
 

 
I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf 
–h”, method is outlined there and I suspect there are a number of discussions 
on it within the emailing list archive that you should search.
 
Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
 
From:mohammad agha [mailto:mra...@yahoo.com] 
Sent: Tuesday, 22 November 2011 4:28 AM
To: Dallas Warren
Subject: Re: [gmx-users] density
 
Dear Prof. Warren
 
Excuse me, may I know that how to obtain the average radial density functions 
relative to the center of mass with g_rdf?
I think these plots are produced by counting the number of selected atoms that 
are within the x angstrom wide shells around the micelle COM, and I think that 
I should use from : N= 4 π ρ∫ 0 00  r2 g(r) dr. , but I don't know how to find 
N and what is the computation carefully?
Please help me.
 
Best Regards
Sara


 
From:Dallas Warren 
To: mohammad agha ; Discussion list for GROMACS users 
 
Sent: Monday, November 21, 2011 2:04 AM
Subject: RE: [gmx-users] density
Last bit here, that is probably done using a RDF, which is a probability 
function, which you can then convert into a number of atoms in each shell.
 
Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
 
From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of mohammad agha
Sent: Sunday, 20 November 2011 5:52 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] density
 
Dear Prof. 
 
I have problems about density. I equilibrated my system consist 500 surfactants 
and 6 water molecules in martini coarse-grained for 120 ns and my results 
of g_energy next pr.mdp for density are:
 
average = 907.701
err.est = 0.61
rmsd = 2.54989
tot-drift = -3.4173
 
I don't know about good quantity of err.est, rmsd and tot-drift for density 
adjustment? and when my system has been equilibrated?
May I know about my problem, please?
 
On the other hand, "density distribution for different groups of the system in 
terms of their distance from micell's COM distance"  is considered In the 
articles about surfactants. I think that it is possible with g_density but this 
program compute the density as the function of  box(nm). May I know about this 
problem, Please?
 
Best Regards
sara
 
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RE: [gmx-users] density

[Dallas Warren]

I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf 
–h”, method is outlined there and I suspect there are a number of discussions 
on it within the emailing list archive that you should search.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: mohammad agha [mailto:mra...@yahoo.com]
Sent: Tuesday, 22 November 2011 4:28 AM
To: Dallas Warren
Subject: Re: [gmx-users] density

Dear Prof. Warren

Excuse me, may I know that how to obtain the average radial density functions 
relative to the center of mass with g_rdf?
I think these plots are produced by counting the number of selected atoms that 
are within the x angstrom wide shells around the micelle COM, and I think that 
I should use from : N= 4 π ρ∫ 0 00  r2 g(r) dr. , but I don't know how to find 
N and what is the computation carefully?
Please help me.

Best Regards
Sara

From: Dallas Warren mailto:dallas.war...@monash.edu>>
To: mohammad agha mailto:mra...@yahoo.com>>; Discussion list 
for GROMACS users mailto:gmx-users@gromacs.org>>
Sent: Monday, November 21, 2011 2:04 AM
Subject: RE: [gmx-users] density
Last bit here, that is probably done using a RDF, which is a probability 
function, which you can then convert into a number of atoms in each shell.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu<mailto:dallas.war...@monash.edu>
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org<mailto:gmx-users-boun...@gromacs.org> 
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha
Sent: Sunday, 20 November 2011 5:52 PM
To: gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>
Subject: [gmx-users] density

Dear Prof.

I have problems about density. I equilibrated my system consist 500 surfactants 
and 6 water molecules in martini coarse-grained for 120 ns and my results 
of g_energy next pr.mdp for density are:

average = 907.701
err.est = 0.61
rmsd = 2.54989
tot-drift = -3.4173

I don't know about good quantity of err.est, rmsd and tot-drift for density 
adjustment? and when my system has been equilibrated?
May I know about my problem, please?

On the other hand, "density distribution for different groups of the system in 
terms of their distance from micell's COM distance"  is considered In the 
articles about surfactants. I think that it is possible with g_density but this 
program compute the density as the function of  box(nm). May I know about this 
problem, Please?

Best Regards
sara

-- 
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RE: [gmx-users] density

[Dallas Warren]

Last bit here, that is probably done using a RDF, which is a probability 
function, which you can then convert into a number of atoms in each shell.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of mohammad agha
Sent: Sunday, 20 November 2011 5:52 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] density

Dear Prof.

I have problems about density. I equilibrated my system consist 500 surfactants 
and 6 water molecules in martini coarse-grained for 120 ns and my results 
of g_energy next pr.mdp for density are:

average = 907.701
err.est = 0.61
rmsd = 2.54989
tot-drift = -3.4173

I don't know about good quantity of err.est, rmsd and tot-drift for density 
adjustment? and when my system has been equilibrated?
May I know about my problem, please?

On the other hand, "density distribution for different groups of the system in 
terms of their distance from micell's COM distance"  is considered In the 
articles about surfactants. I think that it is possible with g_density but this 
program compute the density as the function of  box(nm). May I know about this 
problem, Please?

Best Regards
sara
-- 
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[gmx-users] density

[mohammad agha]

Dear Prof. 


I have problems about density. I equilibrated my system consist 500 surfactants 
and 6 water molecules in martini coarse-grained for 120 ns and my results 
of g_energy next pr.mdp for density are:

average = 907.701
err.est = 0.61
rmsd = 2.54989
tot-drift = -3.4173

I don't know about good quantity of err.est, rmsd and tot-drift for density 
adjustment? and when my system has been equilibrated?
May I know about my problem, please?

On the other hand, "density distribution for different groups of the system in 
terms of their distance from micell's COM distance"  is considered In the 
articles about surfactants. I think that it is possible with g_density but this 
program compute the density as the function of  box(nm). May I know about this 
problem, Please?

Best Regards
sara
-- 
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Re: [gmx-users] Density

[Justin A. Lemkul]

vferra...@units.it wrote:

Dear all,

I want to calculate the density of my system and visualize it during the 
simulation time. I've tried with g_density and with g_energy but in all 
the cases the density calculated is the average density all along the 
simulation and not the density of all the system in each step of the 
trajectory. How can I compute what I need?




g_energy should have printed an energy.xvg file that contains values printed 
every nstenergy steps.  It will not necessarily agree exactly with the average 
printed by g_energy, since the .edr file is accurate over all MD steps but the 
.xvg file contains data saved at only the requested output frequency.  So unless 
you set nstenergy = 1, you will not get density values over every step.


-Justin


Thanks a lot.
Valerio


This message was sent using IMP, the Internet Messaging Program.




--


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] Density

[vferrario]

Dear all,

I want to calculate the density of my system and visualize it during  
the simulation time. I've tried with g_density and with g_energy but  
in all the cases the density calculated is the average density all  
along the simulation and not the density of all the system in each  
step of the trajectory. How can I compute what I need?


Thanks a lot.
Valerio


This message was sent using IMP, the Internet Messaging Program.


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Re: [gmx-users] density off

[David van der Spoel]

On 2011-04-20 20.10, Juliette N. wrote:

Hi David,

I used to apply NPT to fix the density, how can I get the denisty using NVT?


You turn off P coupling and fix the right density by scaling using editconf.


On 20 April 2011 13:46, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote:

On 2011-04-20 19.40, Juliette N. wrote:

Hello,

I am trying to obtain the density for my system that is exactly
identical to experimental value but whatever pressure I apply
density is
still off by 3%.
Is this issue common?
--
Thanks,
Jennifer N.

Yes, force fields are not perfect.
How about running NVT at the experimental density and measuring the
pressure?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
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--
Thanks,
Jennifer N.




--
David van der Spoel, Ph.D., Professor of Biology
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] density off

[Juliette N.]

Hi David,

I used to apply NPT to fix the density, how can I get the denisty using NVT?

On 20 April 2011 13:46, David van der Spoel  wrote:

> On 2011-04-20 19.40, Juliette N. wrote:
>
>> Hello,
>>
>> I am trying to obtain the density for my system that is exactly
>> identical to experimental value but whatever pressure I apply density is
>> still off by 3%.
>> Is this issue common?
>> --
>> Thanks,
>> Jennifer N.
>>
>>  Yes, force fields are not perfect.
> How about running NVT at the experimental density and measuring the
> pressure?
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-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!
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> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Thanks,
Jennifer N.
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Re: [gmx-users] density off

[David van der Spoel]

On 2011-04-20 19.40, Juliette N. wrote:

Hello,

I am trying to obtain the density for my system that is exactly
identical to experimental value but whatever pressure I apply density is
still off by 3%.
Is this issue common?
--
Thanks,
Jennifer N.


Yes, force fields are not perfect.
How about running NVT at the experimental density and measuring the 
pressure?


--
David van der Spoel, Ph.D., Professor of Biology
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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[gmx-users] density off

[Juliette N.]

Hello,

I am trying to obtain the density for my system that is exactly identical to
experimental value but whatever pressure I apply density is still off by 3%.

Is this issue common?
-- 
Thanks,
Jennifer N.
-- 
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Re: [gmx-users] Density Differences

[Kavyashree M]

Ok Thanks.

On Wed, Apr 13, 2011 at 6:22 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
>> stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
>> close to the value i have got. (1.025g/cc). or is this value tolerable?
>>
>>
> That's a 2.6% difference.  I wouldn't call that "nowhere close."  Unless
> you are literally reproducing the exact same system used during
> parameterization (which you're not, based on your system contents and the
> use of algorithms like PME that didn't exist in 1983) then you shouldn't
> necessarily expect identical results.
>
> -Justin
>
>
>> On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Kavyashree M wrote:
>>
>>I am sorry I did not include it in the mail: i used the following:
>>
>>pcoupl  = Parrinello_Rahmanpcoupltype
>>   = isotropictau_p   = 2.0
>>   compressibility = 4.5e-5ref_p
>>  = 1.0  I agree that density of water is
>> different  depending on the
>>model used,
>>so for tip4p water what is the range of fluctuations accepted?
>>So that
>>we can conclude that the difference is not due to any other
>>reason but
>>the water model used.
>>
>>
>>The extent of fluctuation in any pressure-related term depends on
>>the size of your system and several of the .mdp settings.
>>
>>http://www.gromacs.org/Documentation/Terminology/Pressure
>>
>>For the actual target value of TIP4P density, refer to the
>>literature.  The TIP4P citation is provided in the Gromacs manual.
>>
>>-Justin
>>
>>Thanking you
>>With regards
>>Kavya
>>
>>On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Kavyashree M wrote:
>>
>>   Dear gromacs users,
>>I am trying to simulate a 225aa protein at 300K in water,
>>   with OPLSAA force filed, tip4p water model, using the
>>   parameters below (for pressure equilibration) during
>>
>>
>>   You're not doing NPT.  You haven't specified pcoupl or any of
>> the
>>   other relevant parameters, so you're doing NVT.
>>
>>
>>   position restrained md.
>>
>>   integrator  = md  dt
>>= 0.002nsteps
>> = 5  nstcomm = 10
>>  nstlist= 5 ns_type
>> = grid  pbc= xyz
>> rlist  = 1.40
>>   coulombtype = PME  rcoulomb=
>>1.40vdwtype = Switch
>>  rvdw_switch= 0.9  rvdw
>>   = 1.00fourierspacing  =
>>0.12  pme_order  = 4
>>   ewald_rtol  = 1e-5
>> optimize_fft= yes Tcoupl =
>>nose-hoover   tc_grps = Protein  Non-Protein
>>   tau_t   = 0.4  0.4 ref_t
>> = 300  300nh-chain-length
>>  = 1gen_vel = no continuation
>> = yes  constraints = all-bonds
>>   constraint-algorithm= LINCS
>>   lincs-order = 4lincs-iter
>>   =
>>   1   lincs-warnangle = 30
>>   when I calculate the densities, the average came out to be
>>   1025.91 kg/m^3,
>>   Could anyone please clarify me the reason for this density.
>>
>>
>>   Simulating with the right ensemble (NPT) will equilibrate the
>>   pressure and thus density.  As a fundamental point, please also
>>   realize that each water model has its own (different) expected
>>   density value, which is also influenced somewhat by the
>> remaining
>>   contents of the system.  Therefore, the result you obtain may
>>not be
>>   in exact agreement with experimental bulk density of water.
>>
>>   -Justin
>>
>>
>>   Thanking you
>>   With regards
>>   Kavya
>>
>>
>>   -- 
>>
>>   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
>>
>>   htt

Re: [gmx-users] Density Differences

[Justin A. Lemkul]

Kavyashree M wrote:

The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?



That's a 2.6% difference.  I wouldn't call that "nowhere close."  Unless you are 
literally reproducing the exact same system used during parameterization (which 
you're not, based on your system contents and the use of algorithms like PME 
that didn't exist in 1983) then you shouldn't necessarily expect identical results.


-Justin



On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

I am sorry I did not include it in the mail: i used the following:

pcoupl  = Parrinello_Rahmanpcoupltype  
   = isotropictau_p   = 2.0
 compressibility = 4.5e-5ref_p  
= 1.0  
I agree that density of water is different  depending on the

model used,
so for tip4p water what is the range of fluctuations accepted?
So that
we can conclude that the difference is not due to any other
reason but
the water model used.


The extent of fluctuation in any pressure-related term depends on
the size of your system and several of the .mdp settings.

http://www.gromacs.org/Documentation/Terminology/Pressure

For the actual target value of TIP4P density, refer to the
literature.  The TIP4P citation is provided in the Gromacs manual.

-Justin

Thanking you
With regards
Kavya

On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Kavyashree M wrote:

   Dear gromacs users,
I am trying to simulate a 225aa protein at 300K in water,
   with OPLSAA force filed, tip4p water model, using the
   parameters below (for pressure equilibration) during


   You're not doing NPT.  You haven't specified pcoupl or any of the
   other relevant parameters, so you're doing NVT.


   position restrained md.

   integrator  = md  dt
= 0.002nsteps  
   = 5  nstcomm = 10
  nstlist= 5
 ns_type = grid  pbc
= xyz rlist  = 1.40

   coulombtype = PME  rcoulomb=
1.40vdwtype = Switch  
rvdw_switch= 0.9  rvdw  
 = 1.00fourierspacing  =
0.12  pme_order  = 4
 ewald_rtol  = 1e-5
 optimize_fft= yes Tcoupl =

nose-hoover   tc_grps = Protein  Non-Protein
   tau_t   = 0.4  0.4 ref_t
 = 300  300nh-chain-length  
  = 1gen_vel = no continuation  
 = yes  constraints = all-bonds

   constraint-algorithm= LINCS
   lincs-order = 4lincs-iter
 =

   1   lincs-warnangle = 30
   when I calculate the densities, the average came out to be
   1025.91 kg/m^3,
   Could anyone please clarify me the reason for this density.


   Simulating with the right ensemble (NPT) will equilibrate the
   pressure and thus density.  As a fundamental point, please also
   realize that each water model has its own (different) expected
   density value, which is also influenced somewhat by the remaining
   contents of the system.  Therefore, the result you obtain may
not be
   in exact agreement with experimental bulk density of water.

   -Justin


   Thanking you
   With regards
   Kavya


   -- 

   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

   ===

Re: [gmx-users] Density Differences

[Kavyashree M]

The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?


On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> I am sorry I did not include it in the mail: i used the following:
>>
>> pcoupl  = Parrinello_Rahmanpcoupltype  =
>> isotropictau_p   = 2.0
>>  compressibility = 4.5e-5ref_p   = 1.0
>>
>> I agree that density of water is different  depending on the model used,
>> so for tip4p water what is the range of fluctuations accepted? So that
>> we can conclude that the difference is not due to any other reason but
>> the water model used.
>>
>>
> The extent of fluctuation in any pressure-related term depends on the size
> of your system and several of the .mdp settings.
>
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> For the actual target value of TIP4P density, refer to the literature.  The
> TIP4P citation is provided in the Gromacs manual.
>
> -Justin
>
>  Thanking you
>> With regards
>> Kavya
>>
>> On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Kavyashree M wrote:
>>
>>Dear gromacs users,
>> I am trying to simulate a 225aa protein at 300K in water,
>>with OPLSAA force filed, tip4p water model, using the
>>parameters below (for pressure equilibration) during
>>
>>
>>You're not doing NPT.  You haven't specified pcoupl or any of the
>>other relevant parameters, so you're doing NVT.
>>
>>
>>position restrained md.
>>
>>integrator  = md  dt
>>   = 0.002nsteps  = 5
>>  nstcomm = 10   nstlist
>>= 5  ns_type = grid  pbc
>> = xyz rlist  = 1.40
>>coulombtype = PME  rcoulomb= 1.40
>>  vdwtype = Switch   rvdw_switch
>>= 0.9  rvdw= 1.00
>>  fourierspacing  = 0.12  pme_order
>>  = 4  ewald_rtol  = 1e-5
>>  optimize_fft= yes Tcoupl = nose-hoover
>>   tc_grps = Protein  Non-Protein
>>tau_t   = 0.4  0.4 ref_t
>>= 300  300nh-chain-length = 1
>>  gen_vel = no continuation= yes
>>  constraints = all-bonds
>>constraint-algorithm= LINCS
>>lincs-order = 4lincs-iter  =
>>1   lincs-warnangle = 30
>>when I calculate the densities, the average came out to be
>>1025.91 kg/m^3,
>>Could anyone please clarify me the reason for this density.
>>
>>
>>Simulating with the right ensemble (NPT) will equilibrate the
>>pressure and thus density.  As a fundamental point, please also
>>realize that each water model has its own (different) expected
>>density value, which is also influenced somewhat by the remaining
>>contents of the system.  Therefore, the result you obtain may not be
>>in exact agreement with experimental bulk density of water.
>>
>>-Justin
>>
>>
>>Thanking you
>>With regards
>>Kavya
>>
>>
>>-- 
>>
>>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
>>
>>
>>-- gmx-users mailing listgmx-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
>>
>>
>>
> --
> 
>
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the arc

Re: [gmx-users] Density Differences

[Justin A. Lemkul]

Kavyashree M wrote:

I am sorry I did not include it in the mail: i used the following:

pcoupl  = Parrinello_Rahman
pcoupltype  = isotropic
tau_p   = 2.0  
compressibility = 4.5e-5
ref_p   = 1.0  


I agree that density of water is different  depending on the model used,
so for tip4p water what is the range of fluctuations accepted? So that
we can conclude that the difference is not due to any other reason but
the water model used.



The extent of fluctuation in any pressure-related term depends on the size of 
your system and several of the .mdp settings.


http://www.gromacs.org/Documentation/Terminology/Pressure

For the actual target value of TIP4P density, refer to the literature.  The 
TIP4P citation is provided in the Gromacs manual.


-Justin


Thanking you
With regards
Kavya

On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Dear gromacs users,
 I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during


You're not doing NPT.  You haven't specified pcoupl or any of the
other relevant parameters, so you're doing NVT.


position restrained md.

integrator  = md  dt
 = 0.002nsteps  = 5
  nstcomm = 10   nstlist
= 5  ns_type = grid
  pbc = xyz rlist  
= 1.40
coulombtype = PME  rcoulomb= 1.40  
  vdwtype = Switch   rvdw_switch
= 0.9  rvdw= 1.00  
  fourierspacing  = 0.12  pme_order
  = 4  ewald_rtol  = 1e-5  
optimize_fft= yes Tcoupl
 = nose-hoover   tc_grps = Protein  Non-Protein
tau_t   = 0.4  0.4 ref_t
  = 300  300nh-chain-length = 1
gen_vel = no continuation= yes  
constraints = all-bonds

constraint-algorithm= LINCS
lincs-order = 4lincs-iter  =
1   lincs-warnangle = 30
when I calculate the densities, the average came out to be
1025.91 kg/m^3,
Could anyone please clarify me the reason for this density.


Simulating with the right ensemble (NPT) will equilibrate the
pressure and thus density.  As a fundamental point, please also
realize that each water model has its own (different) expected
density value, which is also influenced somewhat by the remaining
contents of the system.  Therefore, the result you obtain may not be
in exact agreement with experimental bulk density of water.

-Justin


Thanking you
With regards
Kavya


-- 



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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--


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] Density Differences

[Kavyashree M]

I am sorry I did not include it in the mail: i used the following:

pcoupl  = Parrinello_Rahman
pcoupltype  = isotropic
tau_p   = 2.0
compressibility = 4.5e-5
ref_p   = 1.0

I agree that density of water is different  depending on the model used,
so for tip4p water what is the range of fluctuations accepted? So that
we can conclude that the difference is not due to any other reason but
the water model used.

Thanking you
With regards
Kavya

On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>  I am trying to simulate a 225aa protein at 300K in water,
>> with OPLSAA force filed, tip4p water model, using the
>> parameters below (for pressure equilibration) during
>>
>
> You're not doing NPT.  You haven't specified pcoupl or any of the other
> relevant parameters, so you're doing NVT.
>
>
>  position restrained md.
>>
>> integrator  = md  dt  =
>> 0.002nsteps  = 5   nstcomm
>>   = 10   nstlist = 5
>>  ns_type = grid   pbc = xyz
>> rlist   = 1.40
>> coulombtype = PME  rcoulomb= 1.40 vdwtype
>> = Switch   rvdw_switch = 0.9
>>  rvdw= 1.00 fourierspacing  =
>> 0.12  pme_order   = 4  ewald_rtol
>>= 1e-5   optimize_fft= yes Tcoupl
>>  = nose-hoover   tc_grps = Protein  Non-Protein
>> tau_t   = 0.4  0.4 ref_t   =
>> 300  300nh-chain-length = 1 gen_vel
>> = no continuation= yes   constraints = all-bonds
>> constraint-algorithm= LINCS
>> lincs-order = 4lincs-iter  = 1
>>   lincs-warnangle = 30
>> when I calculate the densities, the average came out to be 1025.91 kg/m^3,
>> Could anyone please clarify me the reason for this density.
>>
>>
> Simulating with the right ensemble (NPT) will equilibrate the pressure and
> thus density.  As a fundamental point, please also realize that each water
> model has its own (different) expected density value, which is also
> influenced somewhat by the remaining contents of the system.  Therefore, the
> result you obtain may not be in exact agreement with experimental bulk
> density of water.
>
> -Justin
>
>
>  Thanking you
>> With regards
>> Kavya
>>
>>
> --
> 
>
> 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
>
> 
> --
> gmx-users mailing listgmx-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!
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Re: [gmx-users] Density Differences

[Justin A. Lemkul]

Kavyashree M wrote:

Dear gromacs users,
 
I am trying to simulate a 225aa protein at 300K in water,

with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during


You're not doing NPT.  You haven't specified pcoupl or any of the other relevant 
parameters, so you're doing NVT.



position restrained md.

integrator  = md  
dt  = 0.002
nsteps  = 5   
nstcomm = 10   
nstlist = 5  
ns_type = grid   
pbc = xyz 
rlist   = 1.40
coulombtype = PME  
rcoulomb= 1.40 
vdwtype = Switch   
rvdw_switch = 0.9  
rvdw= 1.00 
fourierspacing  = 0.12  
pme_order   = 4  
ewald_rtol  = 1e-5   
optimize_fft= yes 
Tcoupl  = nose-hoover   
tc_grps = Protein  Non-Protein
tau_t   = 0.4  0.4 
ref_t   = 300  300
nh-chain-length = 1 
gen_vel = no 
continuation= yes   
constraints = all-bonds

constraint-algorithm= LINCS
lincs-order = 4
lincs-iter  = 1   
lincs-warnangle = 30 


when I calculate the densities, the average came out to be 1025.91 kg/m^3,
Could anyone please clarify me the reason for this density.



Simulating with the right ensemble (NPT) will equilibrate the pressure and thus 
density.  As a fundamental point, please also realize that each water model has 
its own (different) expected density value, which is also influenced somewhat by 
the remaining contents of the system.  Therefore, the result you obtain may not 
be in exact agreement with experimental bulk density of water.


-Justin


Thanking you
With regards
Kavya



--


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] Density Differences

[Kavyashree M]

Dear gromacs users,

I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during
position restrained md.

integrator  = md
dt  = 0.002
nsteps  = 5
nstcomm = 10
nstlist = 5
ns_type = grid
pbc = xyz
rlist   = 1.40
coulombtype = PME
rcoulomb= 1.40
vdwtype = Switch
rvdw_switch = 0.9
rvdw= 1.00
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
Tcoupl  = nose-hoover
tc_grps = Protein  Non-Protein
tau_t   = 0.4  0.4
ref_t   = 300  300
nh-chain-length = 1
gen_vel = no
continuation= yes
constraints = all-bonds
constraint-algorithm= LINCS
lincs-order = 4
lincs-iter  = 1
lincs-warnangle = 30

when I calculate the densities, the average came out to be 1025.91 kg/m^3,
Could anyone please clarify me the reason for this density.

Thanking you
With regards
Kavya
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Re: [gmx-users] Density of methanol too low

[David van der Spoel]

On 2011-03-16 16.35, Jesús Carrete Montaña wrote:

Dear list members,

I am running some simple simulations of pure ethanol and methanol using
the opls-aa force field as implemented in GROMACS 4.5.3, as a test case
before attempting to study mixtures with more complex molecules. My
problem is that, even though there are published results [1] that show
that this force field can yield satisfatory estimates of the density of
methanol, I am getting an average density around 745 kg/m3, much lower
than the expected 786 kg/m3.
Attached you can find all the relevant imput files (em.mdp is for the
initial energy minimization, stab.mdp for the "stabilization" run and
run.mdp for the "production" run; sample methanol.gro only contains one
molecule). I got good results for ethanol and ethanol/water mixtures using
basically the same set of mdp files, so I suspect the problem is in my
input .gro file, but I haven't been able to spot it. I would be thankful
for any help you could provide.

Best wishes,
Jesús

[1] G. Kaminski and W. L. Jorgensen, J. Phys. Chem. 1996, 100, 18010-18013.

Check Wensink et al. JCP 119 (2003) 7308. Did you turn on PME, 
dispersion correction etc?


--
David van der Spoel, Ph.D., Professor of Biology
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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[gmx-users] Density of methanol too low

[Jesús Carrete Montaña]

Dear list members,

   I am running some simple simulations of pure ethanol and methanol using
the opls-aa force field as implemented in GROMACS 4.5.3, as a test case
before attempting to study mixtures with more complex molecules. My
problem is that, even though there are published results [1] that show
that this force field can yield satisfatory estimates of the density of
methanol, I am getting an average density around 745 kg/m3, much lower
than the expected 786 kg/m3.
   Attached you can find all the relevant imput files (em.mdp is for the
initial energy minimization, stab.mdp for the "stabilization" run and
run.mdp for the "production" run; sample methanol.gro only contains one
molecule). I got good results for ethanol and ethanol/water mixtures using
basically the same set of mdp files, so I suspect the problem is in my
input .gro file, but I haven't been able to spot it. I would be thankful
for any help you could provide.

Best wishes,
Jesús

[1] G. Kaminski and W. L. Jorgensen, J. Phys. Chem. 1996, 100, 18010-18013.


topol.top
Description: Binary data


stab.mdp
Description: Binary data


run.mdp
Description: Binary data


em.mdp
Description: Binary data


methanol.gro
Description: Binary data
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Re: [gmx-users] Density of water, Dispcorr and rmsd

[Mark Abraham]

On 9/03/2011 10:43 PM, Kavyashree M wrote:

Dear users,

What is the difference between densities predicted by tip4p and 
spc models?
I am using tip4p (with OPLSAA forcefield) in the simulation, during 
position restrained
dynamics, Average water density is around 1015kg-m-3 at 300K which is 
quite far from

expt value..


You're modelling a flexible three-atom two-lone-pair fluid that does 
proton transfer and hydrogen bonding with a non-dissociative rigid 
four-point three-parameter model. 1.5% error starts to sound OK 
actually. If you were actually using position restraints on those water 
molecules, then all you are observing is the density of the starting 
configuration. Anyway, deviations of up to about 20-30 are expected, and 
the size and sign depend on your pressure coupling scheme, the water 
model, and what the water model was parametrized to reproduce.




The Dispersion correction (DIspCorr) is applicable only when we 
use vdw_type = cut off?

Any known disadvantage of using vdw_type = switch?


Please do your homework reading the (for example) the manual and primary 
literature, as suitable.


What could be the possible reasons for getting quite noisy and not 
equilibrating RMSD

of backbone  during MD simulations?


Non-ergodicity of finite simulations, a broken model, an intrinsically 
unstable system, wrong observations, periodicity artefacts, lack of 
experience in judging how significant noise is... anything really :-)


Mark
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[gmx-users] Density of water, Dispcorr and rmsd

[Kavyashree M]

Dear users,

What is the difference between densities predicted by tip4p and spc
models?
I am using tip4p (with OPLSAA forcefield) in the simulation, during position
restrained
dynamics, Average water density is around 1015kg-m-3 at 300K which is quite
far from
expt value..

The Dispersion correction (DIspCorr) is applicable only when we use
vdw_type = cut off?
Any known disadvantage of using vdw_type = switch?

What could be the possible reasons for getting quite noisy and not
equilibrating RMSD
of backbone  during MD simulations?

Thanking you
With Regards
M. Kavyashree
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[gmx-users] Density of the box

[Kavyashree M]

Thank you Tsjerk!

Actually I was not using any dummy atoms or united atoms
in this case. I was using a pdb file with just water atoms (1BP2).

Kindly excuse me I was not recieving any replys to my mail id
ka...@rishi.serc.iisc.ernet.in.
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Re: [gmx-users] Density of the box

[Tsjerk Wassenaar]

Hi,

editconf needs to take the masses from a database file if not fed with
a run input file. It will probably miss out on some types of atoms or
get the masses wrong, especially with united atoms and/or dummies.
Probably the density would be correct giving a .tpr file for input.

Cheers,

Tsjerk

On Mon, Jan 10, 2011 at 4:06 PM,   wrote:
>
>
> Sir,
>
>   I am using Gromacs 4.0.7 version. Does this problem exits
> in other older or newer versions? what is the density of water
> that spc216 adds? If it is a fixed density, then i encountered
> a problem -
>
>
> I tried using 1 water molecule as a system (instead of protein), in a
> cubic box with 0.8nm distance (-d), and filled it with spc216 water,
> in this case the density it showed was 933.221g/l,
>
> 
> Output configuration contains 513 atoms in 171 residues
> Volume                 :     5.48157 (nm^3)
> Density                :     933.221 (g/l)
> Number of SOL molecules:    171
> -
>
> but when I used the same system i.e water, with a cubic box of 1.0nm
> distact from water (-d) and filled with spc216 water it gave a density
> of 1001.85g/l,
>
> --
> Output configuration contains 1017 atoms in 339 residues
> Volume                 :     10.1226 (nm^3)
> Density                :     1001.85 (g/l)
> Number of SOL molecules:    339
> --
>
> So does this trend indicate that the density increases with increase in
> volume of the same system? and spc216 does not add water according to
> a specific density?
>
> With Regards
> MKS
>
>> Hmm, that's the second post in a week reporting editconf giving an
>> apparently spurious measurement of the mass. Sounds like it could be a
>> bug. Thoughts, anyone?
>>
>> Mark
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
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Re: [gmx-users] Density of the box

[kavya]

Sir,

   I am using Gromacs 4.0.7 version. Does this problem exits
in other older or newer versions? what is the density of water
that spc216 adds? If it is a fixed density, then i encountered
a problem -


I tried using 1 water molecule as a system (instead of protein), in a
cubic box with 0.8nm distance (-d), and filled it with spc216 water,
in this case the density it showed was 933.221g/l,


Output configuration contains 513 atoms in 171 residues
Volume : 5.48157 (nm^3)
Density: 933.221 (g/l)
Number of SOL molecules:171
-

but when I used the same system i.e water, with a cubic box of 1.0nm
distact from water (-d) and filled with spc216 water it gave a density
of 1001.85g/l,

--
Output configuration contains 1017 atoms in 339 residues
Volume : 10.1226 (nm^3)
Density: 1001.85 (g/l)
Number of SOL molecules:339
--

So does this trend indicate that the density increases with increase in
volume of the same system? and spc216 does not add water according to
a specific density?

With Regards
MKS

> Hmm, that's the second post in a week reporting editconf giving an
> apparently spurious measurement of the mass. Sounds like it could be a
> bug. Thoughts, anyone?
>
> Mark
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Re: [gmx-users] Density of the box

[Mark Abraham]

On 10/01/2011 7:59 PM, ka...@rishi.serc.iisc.ernet.in wrote:

Dear Gromacs users,

I was trying to run a simulation using a protein of 123  aa long
and wanted to adjust the density to 993.04g/l so with the following
command I ran the editconf:

editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479

Its output was as follows:

--
.
.
Read 1842 atoms
Volume: 115.734 nm^3, corresponds to roughly 52000 electrons
No velocities found
 system size :  3.370  4.749  4.270 (nm)
 diameter:  4.979   (nm)
 center  :  1.646  1.395  2.422 (nm)
 box vectors :  4.707  6.445  3.815 (nm)
 box angles  :  90.00  90.00  90.00 (degrees)
 box volume  : 115.73   (nm^3)
Volume  of input 115.734 (nm^3)
Massof input 42476.2 (a.m.u.)
Density of input 609.444 (g/l)
Scaling all box vectors by 0.848671
new system size :  2.860  4.030  3.624
 shift   :  1.893  2.106  1.234 (nm)
new center  :  3.289  3.289  3.289 (nm)
new box vectors :  6.579  6.579  6.579 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 284.70   (nm^3)

---
My doubt here is it says that the Mass of input is 42476.2 (a.m.u.),
but the mass of protein is 13795.4 Da (according to the protparam with
sequence input). I am not sure whether protparam takes into account
hydrogens. Even with the inclusion of hydrogens (885), the molecular
weight will still be 14686.49Da. So how is 42476.2 a.m.u. comes?


Hmm, that's the second post in a week reporting editconf giving an 
apparently spurious measurement of the mass. Sounds like it could be a 
bug. Thoughts, anyone?


Mark
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[gmx-users] Density of the box

[kavya]

Dear Gromacs users,

I was trying to run a simulation using a protein of 123  aa long
and wanted to adjust the density to 993.04g/l so with the following
command I ran the editconf:

editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479

Its output was as follows:

--
.
.
Read 1842 atoms
Volume: 115.734 nm^3, corresponds to roughly 52000 electrons
No velocities found
system size :  3.370  4.749  4.270 (nm)
diameter:  4.979   (nm)
center  :  1.646  1.395  2.422 (nm)
box vectors :  4.707  6.445  3.815 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  : 115.73   (nm^3)
Volume  of input 115.734 (nm^3)
Massof input 42476.2 (a.m.u.)
Density of input 609.444 (g/l)
Scaling all box vectors by 0.848671
new system size :  2.860  4.030  3.624
shift   :  1.893  2.106  1.234 (nm)
new center  :  3.289  3.289  3.289 (nm)
new box vectors :  6.579  6.579  6.579 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 284.70   (nm^3)

---
My doubt here is it says that the Mass of input is 42476.2 (a.m.u.),
but the mass of protein is 13795.4 Da (according to the protparam with
sequence input). I am not sure whether protparam takes into account
hydrogens. Even with the inclusion of hydrogens (885), the molecular
weight will still be 14686.49Da. So how is 42476.2 a.m.u. comes?

Thank you all in advance
MKS


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[gmx-users] Density question

[teklebrh]

Dear Gromacs Users,

I run an MD simulation of a pure solvent and found out that the  
density of the solvent deviated a little bit from the actual  
experimental data.


MD density is 880g/ml and the experimental data is 866g/ml. Is this  
reasonable for toluene solvent molecules.


I have a hard time of lowering the density to the experimental value.  
I am using ff53a6 gromos force field with rlist=rvwd=rcoulomb=0.9nm.


Is there any advice on this or it is OK.

Thank you

Rob
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Re: [gmx-users] density tip3p

[Zuzana Benkova]

Hi Nisha,I did not try OPLSAA since I need TIP3P model with CHARMM. With this FF hydrogens are also considered as interaction sites. This is not very good combination for GROMACS, but it appeared that the differences are not too big and the time required for simulation with H interacttion side is significantly larger. From my experience rdf is not too sensitive to cut-offs. Try to estimate for instance dielectric constant, dipole moment, diffusion coefficient to be entirely sure. But I think you are getting equlibrated system. Good luckZuzana Dňa 04/01/10, nishap.pa...@utoronto.ca napísal:Hi Zuzana, You are right. I did get my density to ~0.986g/cm3, and I actually came across this other paper by Price and Brooks, and initially they get a density of Tip3p using pme at around 0.979g/cm3, but they tweak some of the parameters in oplsaa to get the correct density. I am not sure if you have tried that and if that helps at all, but also they are using a different simulation package.I am getting good rdf values for the water even with slightly low density, so I guess it is okay.ThanksQuoting Zuzana Benkova :>Hi Nisha,>>I have performed a benchmark simulations of TIP3P water and I still>obtained density 0.984g.cm-3. It looks that this model gives such a>density. If you look at JCP 79, 926, 1983 you will see that the>authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo>other properties, each model of water has some deficiencies. I tried>large number of cut-offs combinations LJ and QQ tyoes of>interactions, but the density did not gange by more than 0.001g.cm-3.>>>Greetings>>Zuzana>>Dňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello,>>    So I looked at the manual and I changed my mdp parameters as>follows to equilibrate at a constant pressure.>> RUN CONTROL PARAMETERS =>integrator   = sd>tinit    = 0>dt   = 0.002>nsteps   = 50>nstcomm  = 1>nstxout  = 0>nstvout  = 0>nstfout  = 0>nstlog   = 500>nstenergy    = 500>nstxtcout    = 0>xtc-precision    = 1000>nstlist  = 5>ns_type  = grid>pbc  = xyz>rlist    = 1.3>coulombtype  = pme>rcoulomb = 1.3>epsilon-r    = 1>vdw-type = switch>rvdw-switch  = 1.0>rvdw = 1.2>DispCorr = EnerPres>fourierspacing   = 0.1>fourier_nx   = 0>fourier_ny   = 0>fourier_nz   = 0>pme_order    = 6>ewald_rtol   = 1e-06>epsilon_surface  = 0>optimize_fft = no>tc_grps  = system>tau_t    = 0.1>ref_t    = 298>Pcoupl   = berendsen>tau_p    = 1.0>compressibility  = 4.5e-05>ref_p    = 1.0>constraints  = all-bonds>constraint-algorithm = Lincs>unconstrained-start  = no>lincs-order  = 4>lincs-warnangle  = 30>lincs-iter   = 1>gen_vel  = yes>gen_temp = 298.0>gen_seed = 173529>>I also tried using mdp parameters as mentioned in some of the gromacs>tutorials. I ran this simulation for 1ns and I am still getting>density around 985g/l, which is low for tip3p water (27nm^3, 900>water molecules). I checked some of the publications and the values>they obtained were ~998g/l. I checked for vacuum in my system, but I>didn't see anything out of the ordinary. Any insights?>>Thanks>>Nisha P>>Quoting nishap.pa...@utoronto.ca:>>>Thanks. I will look up the manual again.Quoting Sander Pronk :>Hi Nisha,>>Looking at your .mdp, there are some issues that might lead to the>>>behavior that you describe:>>>First: you should try to look up the published densities for tip3p>>>water at 300K - they might actually be close to what you get.>>>Second: your neighbor list cut-off (rlist) might be too small to>>>fully contain the charge groups (check the manual, section 7.3.11).>>>Third: You haven't enabled long-range mean field correction for the>>>pressure or energy. Expect the pressure to be strongly dependent on>>>cut-off (see the same section).>>Sander>On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:>>>I have a box (3x3x3nm) of Tip3p water molecules ~900 and thedensity when I create the box using genbox is 997.177g/l. I didenergy minimization run and the potential energy did convergesmoothly, so I did NPT equilibration run of 100ps and I got thedensity value of 975g/l. Why does the density decrease after therun? these are the parameters that I used :RUN CONTROL PARAMETERSintegrator   = mdtinit    = 0dt   = 0.002nsteps   = 5nstcomm   

Re: [gmx-users] density tip3p

[nishap . patel]

Hi Zuzana,

 You are right. I did get my density to ~0.986g/cm3, and I  
actually came across this other paper by Price and Brooks, and  
initially they get a density of Tip3p using pme at around 0.979g/cm3,  
but they tweak some of the parameters in oplsaa to get the correct  
density. I am not sure if you have tried that and if that helps at  
all, but also they are using a different simulation package.


I am getting good rdf values for the water even with slightly low  
density, so I guess it is okay.


Thanks

Quoting Zuzana Benkova :


Hi Nisha,

I have performed a benchmark simulations of TIP3P water and I still
obtained density 0.984g.cm-3. It looks that this model gives such a
density. If you look at JCP 79, 926, 1983 you will see that the
authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo
other properties, each model of water has some deficiencies. I tried
large number of cut-offs combinations LJ and QQ tyoes of
interactions, but the density did not gange by more than 0.001g.cm-3.


Greetings

Zuzana

Dňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello,

    So I looked at the manual and I changed my mdp parameters as
follows to equilibrate at a constant pressure.

 RUN CONTROL PARAMETERS =
integrator   = sd
tinit    = 0
dt   = 0.002
nsteps   = 50
nstcomm  = 1
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy    = 500
nstxtcout    = 0
xtc-precision    = 1000
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist    = 1.3
coulombtype  = pme
rcoulomb = 1.3
epsilon-r    = 1
vdw-type = switch
rvdw-switch  = 1.0
rvdw = 1.2
DispCorr = EnerPres
fourierspacing   = 0.1
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order    = 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
tc_grps  = system
tau_t    = 0.1
ref_t    = 298
Pcoupl   = berendsen
tau_p    = 1.0
compressibility  = 4.5e-05
ref_p    = 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-warnangle  = 30
lincs-iter   = 1
gen_vel  = yes
gen_temp = 298.0
gen_seed = 173529

I also tried using mdp parameters as mentioned in some of the gromacs
tutorials. I ran this simulation for 1ns and I am still getting
density around 985g/l, which is low for tip3p water (27nm^3, 900
water molecules). I checked some of the publications and the values
they obtained were ~998g/l. I checked for vacuum in my system, but I
didn't see anything out of the ordinary. Any insights?

Thanks

Nisha P

Quoting nishap.pa...@utoronto.ca:


Thanks. I will look up the manual again.

Quoting Sander Pronk :


Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the
behavior that you describe:
First: you should try to look up the published densities for tip3p
water at 300K - they might actually be close to what you get.
Second: your neighbor list cut-off (rlist) might be too small to
fully contain the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the
pressure or energy. Expect the pressure to be strongly dependent on
cut-off (see the same section).

Sander


On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:


I have a box (3x3x3nm) of Tip3p water molecules ~900 and the
density when I create the box using genbox is 997.177g/l. I did
energy minimization run and the potential energy did converge
smoothly, so I did NPT equilibration run of 100ps and I got the
density value of 975g/l. Why does the density decrease after the
run? these are the parameters that I used :

RUN CONTROL PARAMETERS
integrator   = md
tinit    = 0
dt   = 0.002
nsteps   = 5
nstcomm  = 0
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstenergy    = 100
nstxtcout    = 0
xtc_precision    = 1000
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist    = 1.1
coulombtype  = pme
rcoulomb = 1.1
epsilon-r    = 1
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 1.0
Tcoupl   = V-rescale
tc-grps  = System
tau_t    = 0.1
ref_t   

Re: [gmx-users] density tip3p

[Zuzana Benkova]

Hi Nisha,I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each model of water has some deficiencies. I tried large number of cut-offs combinations LJ and QQ tyoes of interactions, but the density did not gange by more than 0.001g.cm-3. GreetingsZuzanaDňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello,    So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS =integrator   = sdtinit    = 0dt   = 0.002nsteps   = 50nstcomm  = 1nstxout  = 0nstvout  = 0nstfout  = 0nstlog   = 500nstenergy    = 500nstxtcout    = 0xtc-precision    = 1000nstlist  = 5ns_type  = gridpbc  = xyzrlist    = 1.3coulombtype  = pmercoulomb = 1.3epsilon-r    = 1vdw-type = switchrvdw-switch  = 1.0rvdw = 1.2DispCorr = EnerPresfourierspacing   = 0.1fourier_nx   = 0fourier_ny   = 0fourier_nz   = 0pme_order    = 6ewald_rtol   = 1e-06epsilon_surface  = 0optimize_fft = notc_grps  = systemtau_t    = 0.1ref_t    = 298Pcoupl   = berendsentau_p    = 1.0compressibility  = 4.5e-05ref_p    = 1.0constraints  = all-bondsconstraint-algorithm = Lincsunconstrained-start  = nolincs-order  = 4lincs-warnangle  = 30lincs-iter   = 1gen_vel  = yesgen_temp = 298.0gen_seed = 173529I also tried using mdp parameters as mentioned in some of the gromacs tutorials. I ran this simulation for 1ns and I am still getting density around 985g/l, which is low for tip3p water (27nm^3, 900 water molecules). I checked some of the publications and the values they obtained were ~998g/l. I checked for vacuum in my system, but I didn't see anything out of the ordinary. Any insights?ThanksNisha PQuoting nishap.pa...@utoronto.ca:>Thanks. I will look up the manual again.>>Quoting Sander Pronk :>>>Hi Nisha,Looking at your .mdp, there are some issues that might lead to the>>behavior that you describe:>>First: you should try to look up the published densities for tip3p>>water at 300K - they might actually be close to what you get.>>Second: your neighbor list cut-off (rlist) might be too small to>>fully contain the charge groups (check the manual, section 7.3.11).>>Third: You haven't enabled long-range mean field correction for the>>pressure or energy. Expect the pressure to be strongly dependent on>>cut-off (see the same section).Sander>>On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:>I have a box (3x3x3nm) of Tip3p water molecules ~900 and the>>>density when I create the box using genbox is 997.177g/l. I did>>>energy minimization run and the potential energy did converge>>>smoothly, so I did NPT equilibration run of 100ps and I got the>>>density value of 975g/l. Why does the density decrease after the>>>run? these are the parameters that I used :>>RUN CONTROL PARAMETERS>>>integrator   = md>>>tinit    = 0>>>dt   = 0.002>>>nsteps   = 5>>>nstcomm  = 0>>>nstxout  = 0>>>nstvout  = 0>>>nstfout  = 0>>>nstlog   = 100>>>nstenergy    = 100>>>nstxtcout    = 0>>>xtc_precision    = 1000>>>nstlist  = 5>>>ns-type  = Grid>>>pbc  = xyz>>>rlist    = 1.1>>>coulombtype  = pme>>>rcoulomb = 1.1>>>epsilon-r    = 1>>>vdw-type = switch>>>rvdw-switch  = 0.8>>>rvdw = 1.0>>>Tcoupl   = V-rescale>>>tc-grps  = System>>>tau_t    = 0.1>>>ref_t    = 300>>>Pcoupl   = berendsen>>>tau_p    = 0.5>>>compressibility  = 4e-05>>>ref_p    = 1.0>>>constraints  = all-bonds>>>constraint-algorithm = Lincs>>>unconstrained-start  = no>>>lincs-order  = 4>>>lincs-iter   = 1>>>lincs-warnangle  = 30>>Am I missing something?>>>Thanks>>Nisha Patel>-->>>gmx-users mailing list    gmx-users@gromacs.org>>>http://lists.gromacs.org/mailman/listinfo/gmx-users>>>Please s

Re: [gmx-users] density tip3p

[Mark Abraham]

On 1/04/2010 4:58 AM, nishap.pa...@utoronto.ca wrote:

Hello,

So I looked at the manual and I changed my mdp parameters as follows to
equilibrate at a constant pressure.

RUN CONTROL PARAMETERS =
integrator = sd
tinit = 0
dt = 0.002
nsteps = 50
nstcomm = 1
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 500
nstenergy = 500
nstxtcout = 0
xtc-precision = 1000
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.3
coulombtype = pme
rcoulomb = 1.3
epsilon-r = 1
vdw-type = switch
rvdw-switch = 1.0
rvdw = 1.2
DispCorr = EnerPres
fourierspacing = 0.1
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
optimize_fft = no
tc_grps = system
tau_t = 0.1
ref_t = 298
Pcoupl = berendsen
tau_p = 1.0
compressibility = 4.5e-05
ref_p = 1.0
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
gen_vel = yes
gen_temp = 298.0
gen_seed = 173529

I also tried using mdp parameters as mentioned in some of the gromacs
tutorials. I ran this simulation for 1ns and I am still getting density
around 985g/l, which is low for tip3p water (27nm^3, 900 water
molecules). I checked some of the publications and the values they
obtained were ~998g/l. I checked for vacuum in my system, but I didn't
see anything out of the ordinary. Any insights?


Did they use stochastic dynamics?

Have you equilibrated first before collecting your data?

Mark


Quoting nishap.pa...@utoronto.ca:


Thanks. I will look up the manual again.

Quoting Sander Pronk :


Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the
behavior that you describe:
First: you should try to look up the published densities for tip3p
water at 300K - they might actually be close to what you get.
Second: your neighbor list cut-off (rlist) might be too small to
fully contain the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the
pressure or energy. Expect the pressure to be strongly dependent on
cut-off (see the same section).

Sander


On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:


I have a box (3x3x3nm) of Tip3p water molecules ~900 and the
density when I create the box using genbox is 997.177g/l. I did
energy minimization run and the potential energy did converge
smoothly, so I did NPT equilibration run of 100ps and I got the
density value of 975g/l. Why does the density decrease after the
run? these are the parameters that I used :

RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.002
nsteps = 5
nstcomm = 0
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 0
xtc_precision = 1000
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 1.1
coulombtype = pme
rcoulomb = 1.1
epsilon-r = 1
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0
Tcoupl = V-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
tau_p = 0.5
compressibility = 4e-05
ref_p = 1.0
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30

Am I missing something?
Thanks

Nisha Patel


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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536

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Nisha Patel



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Re: [gmx-users] density tip3p

[nishap . patel]

Hello,

So I looked at the manual and I changed my mdp parameters as  
follows to equilibrate at a constant pressure.


 RUN CONTROL PARAMETERS =
integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 50
nstcomm  = 1
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 500
nstxtcout= 0
xtc-precision= 1000
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.3
coulombtype  = pme
rcoulomb = 1.3
epsilon-r= 1
vdw-type = switch
rvdw-switch  = 1.0
rvdw = 1.2
DispCorr = EnerPres
fourierspacing   = 0.1
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
tc_grps  = system
tau_t= 0.1
ref_t= 298
Pcoupl   = berendsen
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-warnangle  = 30
lincs-iter   = 1
gen_vel  = yes
gen_temp = 298.0
gen_seed = 173529

I also tried using mdp parameters as mentioned in some of the gromacs  
tutorials. I ran this simulation for 1ns and I am still getting  
density around 985g/l, which is low for tip3p water (27nm^3, 900 water  
molecules). I checked some of the publications and the values they  
obtained were ~998g/l. I checked for vacuum in my system, but I didn't  
see anything out of the ordinary. Any insights?


Thanks

Nisha P



Quoting nishap.pa...@utoronto.ca:


Thanks. I will look up the manual again.

Quoting Sander Pronk :


Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the
behavior that you describe:
First: you should try to look up the published densities for tip3p
water at 300K - they might actually be close to what you get.
Second: your neighbor list cut-off (rlist) might be too small to
fully contain the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the
pressure or energy. Expect the pressure to be strongly dependent on
cut-off (see the same section).

Sander


On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:


I have a box (3x3x3nm) of Tip3p water molecules ~900 and the
density when I create the box using genbox is 997.177g/l. I did
energy minimization run and the potential energy did converge
smoothly, so I did NPT equilibration run of 100ps and I got the
density value of 975g/l. Why does the density decrease after the
run? these are the parameters that I used :

RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5
nstcomm  = 0
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 0
xtc_precision= 1000
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 1.1
coulombtype  = pme
rcoulomb = 1.1
epsilon-r= 1
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 1.0
Tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300
Pcoupl   = berendsen
tau_p= 0.5
compressibility  = 4e-05
ref_p= 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30

Am I missing something?
Thanks

Nisha Patel


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Re: [gmx-users] density tip3p

[nishap . patel]

Thanks. I will look up the manual again.

Quoting Sander Pronk :


Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the   
behavior that you describe:
First: you should try to look up the published densities for tip3p   
water at 300K - they might actually be close to what you get.
Second: your neighbor list cut-off (rlist) might be too small to   
fully contain the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the   
pressure or energy. Expect the pressure to be strongly dependent on   
cut-off (see the same section).


Sander


On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:

I have a box (3x3x3nm) of Tip3p water molecules ~900 and the   
density when I create the box using genbox is 997.177g/l. I did   
energy minimization run and the potential energy did converge   
smoothly, so I did NPT equilibration run of 100ps and I got the   
density value of 975g/l. Why does the density decrease after the   
run? these are the parameters that I used :


RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5
nstcomm  = 0
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 0
xtc_precision= 1000
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 1.1
coulombtype  = pme
rcoulomb = 1.1
epsilon-r= 1
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 1.0
Tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300
Pcoupl   = berendsen
tau_p= 0.5
compressibility  = 4e-05
ref_p= 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30

Am I missing something?
Thanks

Nisha Patel


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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536

--
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Re: [gmx-users] density tip3p

[Sander Pronk]

Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the behavior 
that you describe:
First: you should try to look up the published densities for tip3p water at 
300K - they might actually be close to what you get. 
Second: your neighbor list cut-off (rlist) might be too small to fully contain 
the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the pressure or 
energy. Expect the pressure to be strongly dependent on cut-off (see the same 
section).

Sander


On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:

> I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I 
> create the box using genbox is 997.177g/l. I did energy minimization run and 
> the potential energy did converge smoothly, so I did NPT equilibration run of 
> 100ps and I got the density value of 975g/l. Why does the density decrease 
> after the run? these are the parameters that I used :
> 
> RUN CONTROL PARAMETERS
> integrator   = md
> tinit= 0
> dt   = 0.002
> nsteps   = 5
> nstcomm  = 0
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 100
> nstenergy= 100
> nstxtcout= 0
> xtc_precision= 1000
> nstlist  = 5
> ns-type  = Grid
> pbc  = xyz
> rlist= 1.1
> coulombtype  = pme
> rcoulomb = 1.1
> epsilon-r= 1
> vdw-type = switch
> rvdw-switch  = 0.8
> rvdw = 1.0
> Tcoupl   = V-rescale
> tc-grps  = System
> tau_t= 0.1
> ref_t= 300
> Pcoupl   = berendsen
> tau_p= 0.5
> compressibility  = 4e-05
> ref_p= 1.0
> constraints  = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start  = no
> lincs-order  = 4
> lincs-iter   = 1
> lincs-warnangle  = 30
> 
> Am I missing something?
> Thanks
> 
> Nisha Patel
> 
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] density tip3p

[nishap . patel]

I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density  
when I create the box using genbox is 997.177g/l. I did energy  
minimization run and the potential energy did converge smoothly, so I  
did NPT equilibration run of 100ps and I got the density value of  
975g/l. Why does the density decrease after the run? these are the  
parameters that I used :


 RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5
nstcomm  = 0
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 0
xtc_precision= 1000
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 1.1
coulombtype  = pme
rcoulomb = 1.1
epsilon-r= 1
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 1.0
Tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300
Pcoupl   = berendsen
tau_p= 0.5
compressibility  = 4e-05
ref_p= 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30

Am I missing something?
Thanks

Nisha Patel


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Re: [gmx-users] density vs time

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:



Near the end, the values are fluctuating around one. The reason I was 


That would seem right to me.

trying to get density values was may be to try an understand if the 
density computed by gromacs is different for just water system and 
water+one methane system (i.e. gromacs calculates the density using the 
box and total number of molecules in the box, which would be fine for 
water system but for methane+water it would slightly be a little 
different, no?) and may be normalize my rdf using the difference in the 
density factor. Does that make sense?


See the manual, section 8.4, for the method Gromacs uses for computing RDF. 
That's the second time I've posted that today.


-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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Re: [gmx-users] density vs time

[nishap . patel]

I am trying to get an rdf graph actually, and my values are very close  
to one, but not exactly one, and I was wondering if there is some  
normalization issue with g_rdf? These are my values for rdf:


  0  0
 0.002  0
 0.004  0
 0.006  0
 0.008  0
  0.01  0
 0.012  0
 0.014  0
 0.016  0
 0.018  0
  0.02  0
 0.022  0
 0.024  0
 0.026  0
 0.028  0
  0.03  0
 0.032  0
 0.034  0
 0.036  0
 0.038  0
  0.04  0
 0.042  0
 0.044  0
 0.046  0
 0.048  0
  0.05  0
 0.052  0
 0.054  0
 0.056  0
 0.058  0
  0.06  0
 0.062  0
 0.064  0
 0.066  0
 0.068  0
  0.07  0
 0.072  0
 0.074  0
 0.076  0
 0.078  0
  0.08  0
 0.082  0
 0.084  0
 0.086  0
 0.088  0
  0.09  0
 0.092  0
 0.094  0
 0.096  0
 0.098  0
   0.1  0
 0.102  0
 0.104  0
 0.106  0
 0.108  0
  0.11  0
 0.112  0
 0.114  0
 0.116  0
 0.118  0
  0.12  0
 0.122  0
 0.124  0
 0.126  0
 0.128  0
  0.13  0
 0.132  0
 0.134  0
 0.136  0
 0.138  0
  0.14  0
 0.142  0
 0.144  0
 0.146  0
 0.148  0
  0.15  0
 0.152  0
 0.154  0
 0.156  0
 0.158  0
  0.16  0
 0.162  0
 0.164  0
 0.166  0
 0.168  0
  0.17  0
 0.172  0
 0.174  0
 0.176  0
 0.178  0
  0.18  0
 0.182  0
 0.184  0
 0.186  0
 0.188  0
  0.19  0
 0.192  0
 0.194  0
 0.196  0
 0.198  0
   0.2  0
 0.202  0
 0.204  0
 0.206  0
 0.208  0
  0.21  0
 0.212  0
 0.214  0
 0.216  0
 0.218  0
  0.22  0
 0.222  0
 0.224  0
 0.226  0
 0.228  0
  0.23  0
 0.232  0
 0.234  0
 0.236  0
 0.238  0
  0.24  0
 0.242  0
 0.244  0
 0.246  0
 0.248  0
  0.25  0
 0.252  0
 0.254  0
 0.256  0
 0.258  0
  0.26  0
 0.262  0
 0.264  0
 0.266  0
 0.268 3.32195e-05
  0.27 3.27293e-05
 0.272 0.000193501
 0.274 0.000317806
 0.276 0.000689078
 0.278 0.00126578
  0.28 0.00197816
 0.282 0.00348035
 0.284 0.00653762
 0.286  0.038
 0.288   0.016713
  0.29  0.0238596
 0.292  0.0345034
 0.294  0.0528889
 0.296  0.0698775
 0.298  0.0933922
   0.3   0.118079
 0.302   0.156417
 0.304   0.195336
 0.306   0.242149
 0.308   0.287833
  0.31   0.351093
 0.312   0.411434
 0.314   0.473243
 0.316   0.538749
 0.3180.61093
  0.32   0.688108
 0.322   0.756748
 0.324   0.837504
 0.326   0.914596
 0.328   0.993652
  0.33 1.0663
 0.3321.13958
 0.3341.21522
 0.3361.29358
 0.3381.35543
  0.341.42607
 0.3421.49061
 0.3441.54496
 0.3461.59492
 0.3481.64578
  0.35 1.6887
 0.3521.73861
 0.354 1.7676
 0.3561.78996
 0.3581.82775
  0.361.83798
 0.3621.84435
 0.3641.85567
 0.3661.86664
 0.3681.87024
  0.371.86585
 0.3721.85472
 0.3741.84964
 0.3761.84624
 0.3781.82577
  0.38 1.8069
 0.3821.78844
 0.3841.77257
 0.3861.75025
 0.3881.72797
  0.391.69894
 0.3921.67908
 0.394 1.6537
 0.3961.62812
 0.3981.60552
   0.41.57759
 0.4021.55621
 0.4041.53355
 0.4061.49578
 0.4081.48583
  0.411.45567
 0.4121.43467
 0.4141.41543
 0.416 1.3816
 0.4181.36369
  0.421.34185
 0.4221.31562
 0.4241.28986
 0.4261.27127
 0.4281.24739
  0.431.23036
 0.4321.21598
 0.4341.20053
 

RE: [gmx-users] density vs time

[Dallas B. Warren]

g_energy

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of nishap.pa...@utoronto.ca
> Sent: Wednesday, 17 March 2010 8:32 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] density vs time
> 
> Hello,
> 
>  I am simulating one methane molecule in 899 water molecues in the
> box size of 3 3 3 nm (27nm^3). I would like to determine density vs
> time. Is there a way I can do that? I am running my simulation at
> constant Volume i.e. no pressure coupling. I tried using g_density but
> it gives me density vs box(nm).
> 
> Any suggestions would be useful.
> 
> Thanks.
> 
> Nisha P
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
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Re: [gmx-users] density vs time

[Justin A. Lemkul]

Justin A. Lemkul wrote:



nishap.pa...@utoronto.ca wrote:

Hello,

I am simulating one methane molecule in 899 water molecues in the 
box size of 3 3 3 nm (27nm^3). I would like to determine density vs 
time. Is there a way I can do that? I am running my simulation at 
constant Volume i.e. no pressure coupling. I tried using g_density but 
it gives me density vs box(nm).


Any suggestions would be useful.



g_energy stores density information, except in the case of an NVT 
ensemble.  If your box is fixed, so too is the density.




Edit: g_energy prints density, provided it is contained within the .edr file. 
In your case, it will not be.


-Justin

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Ph.D. Candidate
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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] density vs time

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:

Hello,

I am simulating one methane molecule in 899 water molecues in the 
box size of 3 3 3 nm (27nm^3). I would like to determine density vs 
time. Is there a way I can do that? I am running my simulation at 
constant Volume i.e. no pressure coupling. I tried using g_density but 
it gives me density vs box(nm).


Any suggestions would be useful.



g_energy stores density information, except in the case of an NVT ensemble.  If 
your box is fixed, so too is the density.


-Justin


Thanks.

Nisha P



--


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] density vs time

[nishap . patel]

Hello,

I am simulating one methane molecule in 899 water molecues in the  
box size of 3 3 3 nm (27nm^3). I would like to determine density vs  
time. Is there a way I can do that? I am running my simulation at  
constant Volume i.e. no pressure coupling. I tried using g_density but  
it gives me density vs box(nm).


Any suggestions would be useful.

Thanks.

Nisha P

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RE: [gmx-users] density

[Berk Hess]

> Date: Wed, 24 Feb 2010 14:46:17 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] density
> 
> On 2/24/10 2:00 PM, Sander Pronk wrote:
> > You got pretty close to what the density of SPC water is at 298K
> >
> > According to "Temperature dependence of TIP3P, SPC, and TIP4P water from
> > NPT Monte Carlo simulations: Seeking temperatures of maximum density",
> > William L. Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10,
> > Pages 1179 - 1186 (1998)
> > it should be 0.985g/ml, and TIP4P will give you 1.001g/ml.
> >
> > Remember that you're simulating SPC water, not real water.
> >
> 
> Correct, but note that
> 1. Jorgensen uses a funky switch function rather than PME (undocumented, 
> except in my paper JCTC 2 [2006] p. 1)
> 2. Monte Carlo iso MD (although that shouldn't make a difference)

Well, this does make a difference if some interactions are not switched.
MC will see the jump in the potential at the cut-off, whereas MD which
samples according to the forces does not.

Berk

> 3. Long range corrections to the energy, but not to the pressure
> in case you want to reproduce his results :).
> 
> Cheers, David,
> 
> > Sander
> >
> >
> >
> > On Feb 24, 2010, at 13:23 , Sunil Thapa wrote:
> >
> >> Respectable Experts
> >> Grettings
> >> I am studying diffusion of an oxygen molecule in 255 molecule of SPC
> >> water. I need to determine diffusion coefficient at temperature 298 K
> >> and 1 atm pressure. In order to do that
> >> using editconf I scaled the density of the system including oxygen to
> >> 1g/l. I checked the density after energy minimization (steepest
> >> descent) which gave the reading of 0.76 g/l. After that I equilibrated
> >> the system to pressure of 1 bar and temperature of 298 K using NPT
> >> simulation (berendsen). The density reading was 0.98. When I checked
> >> the density table at 298 K, it was about 0.9927 g/l.
> >> I am afraid if my density is not consistent with experimental density
> >> of the system. Is this some bug of gromacs 3.2.1 or my understanding
> >> of thermodynamics is very poor for pressure and liquid density. Please
> >> help me on this.
> >> Should I use the same NPT simulation to derive the experimental
> >> diffusion coefficient ?
> >> Looking forward to hearing from you
> >> Neal, Nepal
> >>
> >>
> >> --
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> >> <mailto:gmx-users@gromacs.org>
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> -- 
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> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
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Re: [gmx-users] density

[David van der Spoel]

On 2/24/10 2:00 PM, Sander Pronk wrote:

You got pretty close to what the density of SPC water is at 298K

According to "Temperature dependence of TIP3P, SPC, and TIP4P water from
NPT Monte Carlo simulations: Seeking temperatures of maximum density",
William L. Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10,
Pages 1179 - 1186 (1998)
it should be 0.985g/ml, and TIP4P will give you 1.001g/ml.

Remember that you're simulating SPC water, not real water.



Correct, but note that
1. Jorgensen uses a funky switch function rather than PME (undocumented, 
except in my paper JCTC 2 [2006] p. 1)

2. Monte Carlo iso MD (although that shouldn't make a difference)
3. Long range corrections to the energy, but not to the pressure
in case you want to reproduce his results :).

Cheers, David,


Sander



On Feb 24, 2010, at 13:23 , Sunil Thapa wrote:


Respectable Experts
Grettings
I am studying diffusion of an oxygen molecule in 255 molecule of SPC
water. I need to determine diffusion coefficient at temperature 298 K
and 1 atm pressure. In order to do that
using editconf I scaled the density of the system including oxygen to
1g/l. I checked the density after energy minimization (steepest
descent) which gave the reading of 0.76 g/l. After that I equilibrated
the system to pressure of 1 bar and temperature of 298 K using NPT
simulation (berendsen). The density reading was 0.98. When I checked
the density table at 298 K, it was about 0.9927 g/l.
I am afraid if my density is not consistent with experimental density
of the system. Is this some bug of gromacs 3.2.1 or my understanding
of thermodynamics is very poor for pressure and liquid density. Please
help me on this.
Should I use the same NPT simulation to derive the experimental
diffusion coefficient ?
Looking forward to hearing from you
Neal, Nepal


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Re: [gmx-users] density

[Sander Pronk]

You got pretty close to what the density of SPC water is at 298K

According to "Temperature dependence of TIP3P, SPC, and TIP4P water from NPT 
Monte Carlo simulations: Seeking temperatures of maximum density", William L. 
Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10, Pages 1179 - 1186 
(1998)
it should be 0.985g/ml, and TIP4P will give you 1.001g/ml. 

Remember that you're simulating SPC water, not real water. 

Sander



On Feb 24, 2010, at 13:23 , Sunil Thapa wrote:

> Respectable Experts
> Grettings
> I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I 
> need to determine diffusion coefficient at temperature 298 K and 1 atm 
> pressure. In order to do that
> using editconf I scaled the density of the system including oxygen to 1g/l. I 
> checked the density after energy minimization (steepest descent) which gave 
> the reading of 0.76 g/l. After that I equilibrated the system to pressure of 
> 1 bar and temperature of 298 K using NPT simulation (berendsen). The density 
> reading was 0.98. When I checked the density table at 298 K, it was about 
> 0.9927 g/l.
> I am afraid if my density is not consistent with experimental density of the 
> system. Is this some bug of gromacs 3.2.1 or my understanding of 
> thermodynamics is very poor for pressure and liquid density. Please help me 
> on this.
> Should I use the same NPT simulation to derive the experimental diffusion 
> coefficient ?
>  
> Looking forward to hearing from you
> Neal, Nepal
> 
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Re: [gmx-users] density

[David van der Spoel]

On 2/24/10 1:23 PM, Sunil Thapa wrote:

Respectable Experts
Grettings
I am studying diffusion of an oxygen molecule in 255 molecule of SPC
water. I need to determine diffusion coefficient at temperature 298 K
and 1 atm pressure. In order to do that
using editconf I scaled the density of the system including oxygen to
1g/l. I checked the density after energy minimization (steepest descent)
which gave the reading of 0.76 g/l. After that I equilibrated the system
to pressure of 1 bar and temperature of 298 K using NPT simulation
(berendsen). The density reading was 0.98. When I checked the density
table at 298 K, it was about 0.9927 g/l.
I am afraid if my density is not consistent with experimental density of
the system. Is this some bug of gromacs 3.2.1 or my understanding of
thermodynamics is very poor for pressure and liquid density. Please help
me on this.
Should I use the same NPT simulation to derive the experimental
diffusion coefficient ?
Looking forward to hearing from you
Neal, Nepal


It depends on the water model and your settings. Did you use PME and 
long-range corrections for LJ (Dispcorr = EnerPres)?


--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] density

[Sunil Thapa]

Respectable Experts
Grettings
I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I 
need to determine diffusion coefficient at temperature 298 K and 1 atm 
pressure. In order to do that
using editconf I scaled the density of the system including oxygen to 1g/l. I 
checked the density after energy minimization (steepest descent) which gave the 
reading of 0.76 g/l. After that I equilibrated the system to pressure of 1 bar 
and temperature of 298 K using NPT simulation (berendsen). The density reading 
was 0.98. When I checked the density table at 298 K, it was about 0.9927 g/l. 
I am afraid if my density is not consistent with experimental density of the 
system. Is this some bug of gromacs 3.2.1 or my understanding of thermodynamics 
is very poor for pressure and liquid density. Please help me on this. 
Should I use the same NPT simulation to derive the experimental diffusion 
coefficient ?
 
Looking forward to hearing from you
Neal, Nepal


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[gmx-users] density problems when switching from md to sd integrator

[chris . neale]

Dear Aymeric:

1. Can we please see the entire .mdp files for both simulations? I  
suggest that you use a tau_t=1.0 (0.2 is probably over-damped).


2. Although any value of tau_t should still produce the correct  
equilibria, your diffusion rates and your overall sampling may be  
slower with sd tau_t=0.2 than they are with md.


3. Can you reproduce this effect with a box of water?

-- original message --

I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,
compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).
After equilibration and NPT simulation, the system reaches the proper
density reported for the model (791g/L). When I switch to a stochastic
integrator (with inverse friction coeff. tau_t=0.2 ps) the density
rapidly falls to about 765g/L, the potential energy increases, while
temperature and pressure fluctuate much more around their specified
values. I intend to use this box of cyclohexane for solvation free
energy calculations. Can anyone explain what is going on?
Thanks in advance

Aymeric


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[gmx-users] density problems when switching from md to sd integrator

[Aymeric Naômé]

Dear users,

I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K, 
compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds). 
After equilibration and NPT simulation, the system reaches the proper 
density reported for the model (791g/L). When I switch to a stochastic 
integrator (with inverse friction coeff. tau_t=0.2 ps) the density 
rapidly falls to about 765g/L, the potential energy increases, while 
temperature and pressure fluctuate much more around their specified 
values. I intend to use this box of cyclohexane for solvation free 
energy calculations. Can anyone explain what is going on?

Thanks in advance

Aymeric
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Re: [gmx-users] Density

[Justin A. Lemkul]

Carla Jamous wrote:

Thank you Mark, for your answer.
This time I have another issue: temperature.
What are the ways to control temperature in gromacs (during heating or 
equilibration phases), other than temperature coupling?




I don't see how that's even possible.  By definition, temperature control is the 
job of a thermostat.  The sd integrator provides this function as well, by way 
of a Langevin thermostat, but that's really the same thing as using temperature 
coupling, anyway, it's just not a "tcoupl" option.


-Justin


Thank you
Carla

On Thu, Jan 14, 2010 at 10:40 PM, Mark Abraham > wrote:


Carla Jamous wrote:

Hello,
I'm experiencing some difficulties with gromacs. In order to
control my system's density, I have to use g_energy or g_density.


Those tools report density-related quantities, they do not control it.


However, when I use g_energy, in my list, "Density" doesn't appear.


g_energy doesn't report the density if you have a constant-volume
simulation (but grompp probably reported it when you generated the .tpr)


Else, if I use g_density, it needs a file traj.xtc which I don't
have.


Per Erik's point, you can usually use any coordinate file or
trajectory file.

Mark


So please can anyone tell me how to check my system's density in
gromacs?

Thank you

Carla

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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] Density

[Carla Jamous]

Thank you Mark, for your answer.
This time I have another issue: temperature.
What are the ways to control temperature in gromacs (during heating or
equilibration phases), other than temperature coupling?

Thank you
Carla

On Thu, Jan 14, 2010 at 10:40 PM, Mark Abraham wrote:

> Carla Jamous wrote:
>
>> Hello,
>> I'm experiencing some difficulties with gromacs. In order to control my
>> system's density, I have to use g_energy or g_density.
>>
>
> Those tools report density-related quantities, they do not control it.
>
>
>  However, when I use g_energy, in my list, "Density" doesn't appear.
>>
>
> g_energy doesn't report the density if you have a constant-volume
> simulation (but grompp probably reported it when you generated the .tpr)
>
>
>  Else, if I use g_density, it needs a file traj.xtc which I don't have.
>>
>
> Per Erik's point, you can usually use any coordinate file or trajectory
> file.
>
> Mark
>
>
>  So please can anyone tell me how to check my system's density in gromacs?
>>
>> Thank you
>>
>> Carla
>>
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Re: [gmx-users] Density

[Mark Abraham]

Carla Jamous wrote:

Hello,
I'm experiencing some difficulties with gromacs. In order to control my 
system's density, I have to use g_energy or g_density.


Those tools report density-related quantities, they do not control it.


However, when I use g_energy, in my list, "Density" doesn't appear.


g_energy doesn't report the density if you have a constant-volume 
simulation (but grompp probably reported it when you generated the .tpr)



Else, if I use g_density, it needs a file traj.xtc which I don't have.


Per Erik's point, you can usually use any coordinate file or trajectory 
file.


Mark


So please can anyone tell me how to check my system's density in gromacs?

Thank you

Carla


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Re: [gmx-users] Density

[Erik Marklund]

Carla Jamous skrev:

Hello,
I'm experiencing some difficulties with gromacs. In order to control 
my system's density, I have to use g_energy or g_density.

However, when I use g_energy, in my list, "Density" doesn't appear.
Else, if I use g_density, it needs a file traj.xtc which I don't have.

So please can anyone tell me how to check my system's density in gromacs?

Thank you

Carla

Actually, the required input is:
Option Filename  Type Description

 -f   traj.xtc  InputTrajectory: xtc trr trj gro g96 pdb cpt
...

So, if you have a representation of your system in any of the formats 
listed under description, then you're good.


--
---
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Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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[gmx-users] Density

[Carla Jamous]

Hello,
I'm experiencing some difficulties with gromacs. In order to control my
system's density, I have to use g_energy or g_density.
However, when I use g_energy, in my list, "Density" doesn't appear.
Else, if I use g_density, it needs a file traj.xtc which I don't have.

So please can anyone tell me how to check my system's density in gromacs?

Thank you

Carla
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[gmx-users] Density Profile

[afsaneh maleki]

Hi,

 I obtained the electron density profile for the solvent in protein membrane
simulation,

For this I used the following commands:

 ]$ g_density  -f md.xtc  -s md.tpr  -d  z  -dens electron   -o sol.xvg   -ei
electrons.dat   -symm

-n index.ndx

  Although in md.gro file is seen any water in middle box (hydrophobic
region) simulation, Plot shows the electron density of the water is higher
in the middle bilayer  than the edges.

Would any help me to remove this problem?

are commands used correctly?

Best regards,
Afsaneh
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Re: [gmx-users] Density histogram in Ramachandran plot

[Anthony Cruz Balberdi]

Here in the gromacs user contribution:

http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software

I use it once.

Anthony

On Thu, Nov 12, 2009 at 7:49 PM, Mark Abraham  wrote:
> ms wrote:
>>
>> Hi,
>>
>> I wonder if there is an easy way I am missing to get a density histogram
>> from the Ramachandran plot over a trajectory as outputted by g_rama. All
>> I see are big, uniform black blobs and they're not helpful, because with
>> tons of data points a density plot would be much more informative. Thanks!
>
> It's not quite what you want, but using -dt you can have fewer data points.
> Bear in mind that trajectory snapshots "too close" in time aren't
> independent data anyway...
>
> Mark
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Re: [gmx-users] Density histogram in Ramachandran plot

[Mark Abraham]

ms wrote:

Hi,

I wonder if there is an easy way I am missing to get a density histogram
from the Ramachandran plot over a trajectory as outputted by g_rama. All
I see are big, uniform black blobs and they're not helpful, because with
tons of data points a density plot would be much more informative. Thanks!


It's not quite what you want, but using -dt you can have fewer data 
points. Bear in mind that trajectory snapshots "too close" in time 
aren't independent data anyway...


Mark
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[gmx-users] Density histogram in Ramachandran plot

[ms]

Hi,

I wonder if there is an easy way I am missing to get a density histogram
from the Ramachandran plot over a trajectory as outputted by g_rama. All
I see are big, uniform black blobs and they're not helpful, because with
tons of data points a density plot would be much more informative. Thanks!

m.
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Re: [gmx-users] density and intramolecular interactions

[Mark Abraham]

Alexey Odinokov wrote:

Hi everyone,
I have a model for liquid benzene. In this model all bonds are treated as
harmonic potentials. When I use larger constants for these potentials (to
make molecules more planar), the average density of my benzene (from NPT
ensemble) becomes lower. Does virial depend on intramolecular interactions?


See manual Appendix B.


If a want to make benzene molecules completely rigid (through the virtual
sites, for example), can I use the same parameters for intermolecular
interactions?


That depends on how the parameters were developed. In general, assume 
nothing until you've demonstrated they might be transferable to a new 
context.


Mark
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[gmx-users] density and intramolecular interactions

[Alexey Odinokov]

Hi everyone,
I have a model for liquid benzene. In this model all bonds are treated as
harmonic potentials. When I use larger constants for these potentials (to
make molecules more planar), the average density of my benzene (from NPT
ensemble) becomes lower. Does virial depend on intramolecular interactions?
If a want to make benzene molecules completely rigid (through the virtual
sites, for example), can I use the same parameters for intermolecular
interactions?
Thank you in advance,
Alexey
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Re: [gmx-users] Density Problem

[Zhang Hui]

The water box is about 10nm in z direction. x and y box sizes are about
3.3nm.

Hui

On Fri, Apr 24, 2009 at 7:17 PM, Mark Abraham wrote:

> Zhang Hui wrote:
>
>> Dear All,
>>
>> I just found that there is a problem when I extract the density
>> of water from my Gromacs simulations.
>>
>> When I used g_density to get the water density from .trr
>> trajectory file, the density plot looked normal. But when I used trjconv
>> to convert the .trr to .gro file, and then used g_density to get the
>> water density from .gro trajectory file, there was an unusual
>> periodicity in the densities. The density comparison plot is attached.
>>
>> I got the same density pattern by using our own code when
>> taking the .gro file as the input trajectory.  The bin size is .052nm
>> and the gro file is written with 3 decimal places, so there should be
>> enough resolution in the output to avoid artifacts.
>>
>> We are concerned about the integrity of the gro file produced
>> by trjconv because we need to analyze our trajectories and don't know a
>> better alternative than extracting coordinates with trjconv.
>>
>> Below are the scripts I used to convert the .trr to .gro and
>> extract the density:
>>
>>  trjconv -f ***.trr -s ***.tpr -o ***.gro
>>g_density -f ***.trr(***.gro) -s ***.tpr -o density.xvg -number -sl
>> 250
>>
>> The version of Gromacs is 3.3.3, with single precision.
>> Thanks for your help.
>>
>
> How large is the water box? What is the scale of the x-axis in your plots?
>
> Mark
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Re: [gmx-users] Density Problem

[Mark Abraham]

Zhang Hui wrote:

Dear All,

 I just found that there is a problem when I extract the density
of water from my Gromacs simulations.

 When I used g_density to get the water density from .trr
trajectory file, the density plot looked normal. But when I used trjconv
to convert the .trr to .gro file, and then used g_density to get the
water density from .gro trajectory file, there was an unusual
periodicity in the densities. The density comparison plot is attached.

 I got the same density pattern by using our own code when
taking the .gro file as the input trajectory.  The bin size is .052nm
and the gro file is written with 3 decimal places, so there should be
enough resolution in the output to avoid artifacts.

 We are concerned about the integrity of the gro file produced
by trjconv because we need to analyze our trajectories and don't know a
better alternative than extracting coordinates with trjconv.

 Below are the scripts I used to convert the .trr to .gro and
extract the density:

  trjconv -f ***.trr -s ***.tpr -o ***.gro
  
  g_density -f ***.trr(***.gro) -s ***.tpr -o density.xvg -number -sl 250


 The version of Gromacs is 3.3.3, with single precision.
 Thanks for your help.


How large is the water box? What is the scale of the x-axis in your plots?

Mark
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[gmx-users] Density Problem

[Zhang Hui]

Dear All,

 I just found that there is a problem when I extract the density
of water from my Gromacs simulations.

 When I used g_density to get the water density from .trr
trajectory file, the density plot looked normal. But when I used trjconv
to convert the .trr to .gro file, and then used g_density to get the
water density from .gro trajectory file, there was an unusual
periodicity in the densities. The density comparison plot is attached.

 I got the same density pattern by using our own code when
taking the .gro file as the input trajectory.  The bin size is .052nm
and the gro file is written with 3 decimal places, so there should be
enough resolution in the output to avoid artifacts.

 We are concerned about the integrity of the gro file produced
by trjconv because we need to analyze our trajectories and don't know a
better alternative than extracting coordinates with trjconv.

 Below are the scripts I used to convert the .trr to .gro and
extract the density:

  trjconv -f ***.trr -s ***.tpr -o ***.gro

  g_density -f ***.trr(***.gro) -s ***.tpr -o density.xvg -number -sl 250

 The version of Gromacs is 3.3.3, with single precision.
 Thanks for your help.


Hui Zhang
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[gmx-users] Density Problem

[Zhang Hui]

Dear All,

 I just found that there is a problem when I extract the density
of water from my Gromacs simulations.

 When I used g_density to get the water density from .trr
trajectory file, the density plot looked normal. But when I used trjconv
to convert the .trr to .gro file, and then used g_density to get the
water density from .gro trajectory file, there was an unusual
periodicity in the densities. The density comparison plot is attached.

 I got the same density pattern by using our own code when
taking the .gro file as the input trajectory.  The bin size is .052nm
and the gro file is written with 3 decimal places, so there should be
enough resolution in the output to avoid artifacts.

 We are concerned about the integrity of the gro file produced
by trjconv because we need to analyze our trajectories and don't know a
better alternative than extracting coordinates with trjconv.

 Below are the scripts I used to convert the .trr to .gro and
extract the density:

  trjconv -f ***.trr -s ***.tpr -o ***.gro

  g_density -f ***.trr(***.gro) -s ***.tpr -o density.xvg -number -sl 250

 The version of Gromacs is 3.3.3, with single precision.
 Thanks for your help.


Hui Zhang
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RE: [gmx-users] density around protein

[Dallas B. Warren]

Or g_sdf

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 
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Re: [gmx-users] density around protein

[Matt Wyczalkowski]

g_sorient returns the number of solvent molecules within a given
distance range of a protein -- it may be what you are looking for.

Matt

2009/4/5 Morteza Khabiri :
> Dear gmxusers
>
> I want to calculate the density of solvent around protein.
> I already tried the commands g_density and g_densmap but the results are
> not the the things that I want. The g_density Compute partial densities
> across the box and g_densmap just give me one black and white photo which
> don't have sense. Is it possible to compute the number of density with
> other commands of gromacs?
>
> Before thanks
>
> Morteza
>
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[gmx-users] density around protein

[Morteza Khabiri]

Dear gmxusers

I want to calculate the density of solvent around protein.
I already tried the commands g_density and g_densmap but the results are
not the the things that I want. The g_density Compute partial densities
across the box and g_densmap just give me one black and white photo which
don't have sense. Is it possible to compute the number of density with
other commands of gromacs?

Before thanks

Morteza

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Re: [gmx-users] density of the bilayer

[Xavier Periole]

On 12 Nov 2008 11:41:54 -
 "minnale " <[EMAIL PROTECTED]> wrote:
 
Thanks for your reply,
In case of water density, starting of the water density will be for some 
time should come straight line in the graph later gradually reducing and goes 
to zero towards centre of the bilayer again it increases and stop going the 
water density. 

but in my case starting water density itself reducing gradually instead of 
coming straight line for while.

is my opinion wrong?

Ok there you seem to be right.

Do you actually do the density only on water? You should give an index to
g_density and choose from it the water or something else.

Is your system centered? I mean the bilayer in the center of the z axis and
therefore the water distributed on both sides.

Do you actually have enough water solvating your balayer and therefore
showing this plateau value before the decrease?

XAvier



how actally I should get the water density plot of the bilayer?
any suggestions would be appreciated

thanks in advance

On Wed, 12 Nov 2008 Xavier Periole wrote :

On 12 Nov 2008 11:13:51 -
 "minnale " <[EMAIL PROTECTED]> wrote:
 Hi users, Intially I have run the simulation of the bilayer for 5ns then 
extended this to 20ns. When analyse density of the bilayer by considering 
trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc 
its showing almost same density values how come it is possible?

I do not see the same values! They seem to fluctuate!
What would be so wrong in having similar values? Looks good to me!
the command line is  g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 
5ns_den.xvg/20ns_den.xvg


density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4) 
5ns_den.xvg 20ns_den.xvg

 0   916.8650 869.8
   0.113182  886.8920.114679  840.058
   0.226364  840.4790.229359  793.811
   0.339547  782.5090.344038  736.194
   0.452729  718.7990.458717  667.985
   0.565911  652.1120.573397  589.507
   0.679093  576.4810.688076  509.389
   0.792275  501.5020.802755  437.914
   0.905457  423.9930.917435  374.713
1.01864  346.6351.03211  314.386
1.13182   266.881.14679  247.738
  1.245   195.441.26147  173.424
1.35819  123.3631.37615  107.955
1.47137  68.32161.49083  51.0066
1.58455  34.01541.60551  21.3937
  --   ----   --   -- 
 ----   --

  --   ----   --
any comments would be appreciated

Thanks in advance  


-
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-


-
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
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Re: Re: [gmx-users] density of the bilayer

[minnale]

  
Thanks for your reply,
In case of water density, starting of the water density will be for some time 
should come straight line in the graph later gradually reducing and goes to 
zero towards centre of the bilayer again it increases and stop going the water 
density. 

but in my case starting water density itself reducing gradually instead of 
coming straight line for while.
is my opinion wrong?

how actally I should get the water density plot of the bilayer?
any suggestions would be appreciated

thanks in advance
 
On Wed, 12 Nov 2008 Xavier Periole wrote :
>On 12 Nov 2008 11:13:51 -
>  "minnale " <[EMAIL PROTECTED]> wrote:
>>  Hi users, Intially I have run the simulation of the bilayer for 5ns then 
>> extended this to 20ns. When analyse density of the bilayer by considering 
>> trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc 
>> its showing almost same density values how come it is possible?
>I do not see the same values! They seem to fluctuate!
>What would be so wrong in having similar values? Looks good to me!
>>the command line is  g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 
>>5ns_den.xvg/20ns_den.xvg
>>
>>density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4)  
>>5ns_den.xvg 20ns_den.xvg
>>  0   916.8650 869.8
>>0.113182  886.8920.114679  840.058
>>0.226364  840.4790.229359  793.811
>>0.339547  782.5090.344038  736.194
>>0.452729  718.7990.458717  667.985
>>0.565911  652.1120.573397  589.507
>>0.679093  576.4810.688076  509.389
>>0.792275  501.5020.802755  437.914
>>0.905457  423.9930.917435  374.713
>> 1.01864  346.6351.03211  314.386
>> 1.13182   266.881.14679  247.738
>>   1.245   195.441.26147  173.424
>> 1.35819  123.3631.37615  107.955
>> 1.47137  68.32161.49083  51.0066
>> 1.58455  34.01541.60551  21.3937
>>   --   ----   --   --   
>> ----   --
>>   --   ----   --
>> any comments would be appreciated
>>
>>Thanks in advance  
>
>-
>XAvier Periole - PhD
>
>- Molecular Dynamics Group -
>Computation and NMR
>University of Groningen
>The Netherlands
>-
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Re: [gmx-users] density of the bilayer

[Xavier Periole]

On 12 Nov 2008 11:13:51 -
 "minnale " <[EMAIL PROTECTED]> wrote:
 
Hi users, 
Intially I have run the simulation of the bilayer for 5ns then extended this 
to 20ns. When analyse density of the bilayer by considering trajectories of 
these different timings one at 5ns.xtc anonther at 20ns.xtc its showing 
almost same density values how come it is possible? 

I do not see the same values! They seem to fluctuate!
What would be so wrong in having similar values? Looks good to me!
the command line is  
g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 5ns_den.xvg/20ns_den.xvg


density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4)  
5ns_den.xvg 20ns_den.xvg

 0   916.8650 869.8
   0.113182  886.8920.114679  840.058
   0.226364  840.4790.229359  793.811
   0.339547  782.5090.344038  736.194
   0.452729  718.7990.458717  667.985
   0.565911  652.1120.573397  589.507
   0.679093  576.4810.688076  509.389
   0.792275  501.5020.802755  437.914
   0.905457  423.9930.917435  374.713
1.01864  346.6351.03211  314.386
1.13182   266.881.14679  247.738
  1.245   195.441.26147  173.424
1.35819  123.3631.37615  107.955
1.47137  68.32161.49083  51.0066
1.58455  34.01541.60551  21.3937
  --   ----   -- 
  --   ----   --

  --   ----   --

any comments would be appreciated


Thanks in advance
   
   
   
   
   
   








-
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
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[gmx-users] density of the bilayer

[minnale]

  
Hi users, 
Intially I have run the simulation of the bilayer for 5ns then extended this to 
20ns. When analyse density of the bilayer by considering trajectories of these 
different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same 
density values how come it is possible? 
the command line is  
g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 5ns_den.xvg/20ns_den.xvg

density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4)  
5ns_den.xvg 20ns_den.xvg
  0   916.8650 869.8
0.113182  886.8920.114679  840.058
0.226364  840.4790.229359  793.811
0.339547  782.5090.344038  736.194
0.452729  718.7990.458717  667.985
0.565911  652.1120.573397  589.507
0.679093  576.4810.688076  509.389
0.792275  501.5020.802755  437.914
0.905457  423.9930.917435  374.713
 1.01864  346.6351.03211  314.386
 1.13182   266.881.14679  247.738
   1.245   195.441.26147  173.424
 1.35819  123.3631.37615  107.955
 1.47137  68.32161.49083  51.0066
 1.58455  34.01541.60551  21.3937
   --   ----   -- 
   --   ----   --
   --   ----   --
 
any comments would be appreciated

Thanks in advance






 
 
 
 
 
 
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Re: [gmx-users] density graph ( density vs time)

[Justin A. Lemkul]

Jochen Hub wrote:



 huan wrote:

I used g_energy before but i just obtained density (y-axis) versus box

length (x axis).



 huan wrote:

Previously i obtained a density (y-axis) versus box length (x axis)

using g_density..


Sounds like a contradition to me... :-)


Indeed; the g_energy output gives the x-axis as time...

-Justin








thanks

--- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:


From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] density graph ( density vs time)
To: [EMAIL PROTECTED], "Discussion list for GROMACS users" 

Date: Tuesday, October 28, 2008, 11:31 PM
 huan wrote:
Dear all, 


Previously i obtained a density (y-axis) versus box

length (x axis) using g_density..

So now i wonder is it there is another way that we can

use other way to obtain a density (y axis) versus time
length (x-axis).
Use g_energy.

-Justin


Thanks..


--- On Tue, 10/28/08, Mark Abraham

<[EMAIL PROTECTED]> wrote:

From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] density graph ( density

vs time)

To: "Discussion list for GROMACS users"



Date: Tuesday, October 28, 2008, 4:46 PM
 huan wrote:

Dear all gmx-users and developers.

I wish to get a density graph with density

versus time

instead of nm, so how can i obtained this?

Please ask a more specific question. We can't

tell
whether your problem 
is knowing what tool to use, how to use it, how to

label
axes of plots 
or something else.


Mark
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Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




  
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.






--


Justin A. Lemkul
Graduate Research Assistant
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] density graph ( density vs time)

[Jochen Hub]

 huan wrote:
> I used g_energy before but i just obtained density (y-axis) versus box
length (x axis).



 huan wrote:
> Previously i obtained a density (y-axis) versus box length (x axis)
using g_density..


Sounds like a contradition to me... :-)





> 
> thanks
> 
> --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
> 
>> From: Justin A. Lemkul <[EMAIL PROTECTED]>
>> Subject: Re: [gmx-users] density graph ( density vs time)
>> To: [EMAIL PROTECTED], "Discussion list for GROMACS users" 
>> 
>> Date: Tuesday, October 28, 2008, 11:31 PM
>>  huan wrote:
>>> Dear all, 
>>>
>>> Previously i obtained a density (y-axis) versus box
>> length (x axis) using g_density..
>>> So now i wonder is it there is another way that we can
>> use other way to obtain a density (y axis) versus time
>> length (x-axis).
>> Use g_energy.
>>
>> -Justin
>>
>>> Thanks..
>>>
>>>
>>> --- On Tue, 10/28/08, Mark Abraham
>> <[EMAIL PROTECTED]> wrote:
>>>> From: Mark Abraham <[EMAIL PROTECTED]>
>>>> Subject: Re: [gmx-users] density graph ( density
>> vs time)
>>>> To: "Discussion list for GROMACS users"
>> 
>>>> Date: Tuesday, October 28, 2008, 4:46 PM
>>>>  huan wrote:
>>>>> Dear all gmx-users and developers.
>>>>>
>>>>> I wish to get a density graph with density
>> versus time
>>>> instead of nm, so how can i obtained this?
>>>>
>>>> Please ask a more specific question. We can't
>> tell
>>>> whether your problem 
>>>> is knowing what tool to use, how to use it, how to
>> label
>>>> axes of plots 
>>>> or something else.
>>>>
>>>> Mark
>>>> ___
>>>> gmx-users mailing listgmx-users@gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>> http://www.gromacs.org/search
>>>> before posting!
>>>> Please don't post (un)subscribe requests to
>> the list.
>>>> Use the 
>>>> www interface or send it to
>> [EMAIL PROTECTED]
>>>> Can't post? Read
>>>> http://www.gromacs.org/mailing_lists/users.php
>>>
>>>   
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>> http://www.gromacs.org/search before posting!
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>> list. Use the 
>>> www interface or send it to
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>> http://www.gromacs.org/mailing_lists/users.php
>> -- 
>> 
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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 listgmx-users@gromacs.org
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> .
> 


-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] density graph ( density vs time)

[hhhh huan]

I used g_energy before but i just obtained density (y-axis) versus box length 
(x axis). now i wish to obtain density vs time

thanks

--- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] density graph ( density vs time)
> To: [EMAIL PROTECTED], "Discussion list for GROMACS users" 
> 
> Date: Tuesday, October 28, 2008, 11:31 PM
>  huan wrote:
> > Dear all, 
> > 
> > Previously i obtained a density (y-axis) versus box
> length (x axis) using g_density..
> > 
> > So now i wonder is it there is another way that we can
> use other way to obtain a density (y axis) versus time
> length (x-axis).
> > 
> 
> Use g_energy.
> 
> -Justin
> 
> > Thanks..
> > 
> > 
> > --- On Tue, 10/28/08, Mark Abraham
> <[EMAIL PROTECTED]> wrote:
> > 
> >> From: Mark Abraham <[EMAIL PROTECTED]>
> >> Subject: Re: [gmx-users] density graph ( density
> vs time)
> >> To: "Discussion list for GROMACS users"
> 
> >> Date: Tuesday, October 28, 2008, 4:46 PM
> >>  huan wrote:
> >>> Dear all gmx-users and developers.
> >>>
> >>> I wish to get a density graph with density
> versus time
> >> instead of nm, so how can i obtained this?
> >>
> >> Please ask a more specific question. We can't
> tell
> >> whether your problem 
> >> is knowing what tool to use, how to use it, how to
> label
> >> axes of plots 
> >> or something else.
> >>
> >> Mark
> >> ___
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> http://www.gromacs.org/search
> >> before posting!
> >> Please don't post (un)subscribe requests to
> the list.
> >> Use the 
> >> www interface or send it to
> [EMAIL PROTECTED]
> >> Can't post? Read
> >> http://www.gromacs.org/mailing_lists/users.php
> > 
> > 
> >   
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> [EMAIL PROTECTED]
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> 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] density graph ( density vs time)

[Justin A. Lemkul]

 huan wrote:
Dear all, 


Previously i obtained a density (y-axis) versus box length (x axis) using 
g_density..

So now i wonder is it there is another way that we can use other way to obtain 
a density (y axis) versus time length (x-axis).



Use g_energy.

-Justin


Thanks..


--- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote:


From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] density graph ( density vs time)
To: "Discussion list for GROMACS users" 
Date: Tuesday, October 28, 2008, 4:46 PM
 huan wrote:

Dear all gmx-users and developers.

I wish to get a density graph with density versus time

instead of nm, so how can i obtained this?

Please ask a more specific question. We can't tell
whether your problem 
is knowing what tool to use, how to use it, how to label
axes of plots 
or something else.


Mark
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--


Justin A. Lemkul
Graduate Research Assistant
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] density graph ( density vs time)

[hhhh huan]

Dear all, 

Previously i obtained a density (y-axis) versus box length (x axis) using 
g_density..

So now i wonder is it there is another way that we can use other way to obtain 
a density (y axis) versus time length (x-axis).

Thanks..


--- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote:

> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] density graph ( density vs time)
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, October 28, 2008, 4:46 PM
>  huan wrote:
> > Dear all gmx-users and developers.
> > 
> > I wish to get a density graph with density versus time
> instead of nm, so how can i obtained this?
> 
> Please ask a more specific question. We can't tell
> whether your problem 
> is knowing what tool to use, how to use it, how to label
> axes of plots 
> or something else.
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list.
> Use the 
> www interface or send it to [EMAIL PROTECTED]
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> http://www.gromacs.org/mailing_lists/users.php


  
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Re: [gmx-users] density graph ( density vs time)

[Jochen Hub]

 huan wrote:
> Dear all gmx-users and developers.
> 
> I wish to get a density graph with density versus time instead of nm, so how 
> can i obtained this?

You could extract the box vectors with g_energy and compute the density
from the volume.

Best,
Jochen

> 
> Thanks.
> 
> 
> 
>   
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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> .
> 


-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] density graph ( density vs time)

[Mark Abraham]

 huan wrote:

Dear all gmx-users and developers.

I wish to get a density graph with density versus time instead of nm, so how 
can i obtained this?


Please ask a more specific question. We can't tell whether your problem 
is knowing what tool to use, how to use it, how to label axes of plots 
or something else.


Mark
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[gmx-users] density graph ( density vs time)

[hhhh huan]

Dear all gmx-users and developers.

I wish to get a density graph with density versus time instead of nm, so how 
can i obtained this?

Thanks.



  
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[gmx-users] density graph 2

[hhhh huan]

Dear all Gmx users and developers,

How can i get a density graph with x-axis is time scale?
I obtained a density graph using g_density which output a graph with density vs 
nm (box size).
 So how can i get a graph with density vs time?

Thanks


  
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Re: [gmx-users] density graph

[hhhh huan]

Thanks Justin, 

I realized my mistake.

I get the kj/mol unit because i use g_energy command and select the density 
option.

thanks

--- On Wed, 10/15/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] density graph
> To: [EMAIL PROTECTED], "Discussion list for GROMACS users" 
> 
> Date: Wednesday, October 15, 2008, 9:07 AM
>  huan wrote:
> > Dear all gmx users and developers, 
> >  Is it correct that in gromacs energy (density graph),
> the y-axis is labelledas kJ/mol, I am wonder it is not a
> density unit.
> 
> In the output that I have from g_density (v 3.3), the the
> .xvg file has the 
> y-axis labeled as:
> 
> yaxis  label "Density (kg/m\S3\N)"
> 
> ...which is a density unit.  Where are you seeing kJ/mol? 
> Which version of 
> Gromacs?  What command did you issue?
> 
> -Justin
> 
> > Thanks
> > 
> > 
> >   
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> [EMAIL PROTECTED]
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> 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] density graph

[Justin A. Lemkul]

 huan wrote:
Dear all gmx users and developers, 
 Is it correct that in gromacs energy (density graph), the y-axis is labelledas kJ/mol, I am wonder it is not a density unit.


In the output that I have from g_density (v 3.3), the the .xvg file has the 
y-axis labeled as:


yaxis  label "Density (kg/m\S3\N)"

...which is a density unit.  Where are you seeing kJ/mol?  Which version of 
Gromacs?  What command did you issue?


-Justin


Thanks


  
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--


Justin A. Lemkul
Graduate Research Assistant
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] density graph

[hhhh huan]

Dear all gmx users and developers, 
 Is it correct that in gromacs energy (density graph), the y-axis is labelled   
 as kJ/mol, I am wonder it is not a density unit.
Thanks


  
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Re: [gmx-users] density and CG MARTINI force field

[Mark Abraham]

merc mertens wrote:

Dear people,

I am trying to use the MARTINI CG force field from Marrink et al. for a 100 
residue protein in water. I use the tools from the Marrink website 
(http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the 
necessary gro and itp files. For solvation of my protein I use the water.gro 
from the same website. However, using editconf/genbox to do so it is difficult 
to judge the density of system. genbox tells me that it is usually around a 
value between 220 and 260 g/l depending on boxsize. As the MARTINI forcefield 
uses a 1-to-4 mapping I think 250 g/l should correspond to 1000 g/l using an 
all-atom representation of my system. Still, I do not know whether these 
density values given by genbox are correct. Is there anyway to check this?


Your structure file should have the size of the box recorded - life is 
easy if it is cubic. Otherwise, add up your molecules and molar masses 
and invoke Avogadro for the mass.


Mark
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[gmx-users] density and CG MARTINI force field

[merc mertens]

Dear people,

I am trying to use the MARTINI CG force field from Marrink et al. for a 100 
residue protein in water. I use the tools from the Marrink website 
(http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the 
necessary gro and itp files. For solvation of my protein I use the water.gro 
from the same website. However, using editconf/genbox to do so it is difficult 
to judge the density of system. genbox tells me that it is usually around a 
value between 220 and 260 g/l depending on boxsize. As the MARTINI forcefield 
uses a 1-to-4 mapping I think 250 g/l should correspond to 1000 g/l using an 
all-atom representation of my system. Still, I do not know whether these 
density values given by genbox are correct. Is there anyway to check this?

Thanks for your help,
Merc
-- 
Pt! Schon vom neuen GMX MultiMessenger gehört?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger
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Re: [gmx-users] density calculation of genbox

[Tobias Unruh]

Mark, thank you for reply!

In the output file of genbox the 'right' box size is written:
   8.8   8.8   8.8

Tobias

On Fri, 7 Mar 2008, Mark Abraham wrote:


Tobias Unruh wrote:

Hi,

I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane 
(C32H66) molecules (molecular weight: 450.88 g/mol). This gives a density 
of 793.23 g/l. But genbox calculates 743.576 g/l. The atom masses and 
numbers of atoms are ok in the input .gro file.


Some suggestions?


Check the final line of your .gro file for the actual box sizes.

Mark
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Re: [gmx-users] density calculation of genbox

[Mark Abraham]

Tobias Unruh wrote:

Hi,

I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane 
(C32H66) molecules (molecular weight: 450.88 g/mol). This gives a 
density of 793.23 g/l. But genbox calculates 743.576 g/l. The atom 
masses and numbers of atoms are ok in the input .gro file.


Some suggestions?


Check the final line of your .gro file for the actual box sizes.

Mark
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[gmx-users] density calculation of genbox

[Tobias Unruh]

Hi,

I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane (C32H66) 
molecules (molecular weight: 450.88 g/mol). This gives a density of 793.23 g/l. 
But genbox calculates 743.576 g/l. The atom masses and numbers of atoms are ok 
in the input .gro file.


Some suggestions?

Best regards

Tobias

--
Tobias Unruh
TU Muenchen, FRM-II
85747 Garching, Germany
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Re: [gmx-users] Density Deferences between spc216 and tip4p water models

[Jochen Hub]

[EMAIL PROTECTED] wrote:

Dear All,
I was trying  create a  box (cubic 10 10 10) of water. I am a bit
surprised by looking at the density deferences between spc216 and tip4p
water models. I am giving the brief output below.

genbox -cs tip4p.gro -box 10 10 10

Output configuration contains 131540 atoms in 32885 residues
Volume :1000 (nm^3)
Density: 1639.65 (g/l)
Number of SOL molecules:  32885
  
Theres is something wrong in your calculation of the density. From 32885 
Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l.


Cheers, Jochen


genbox -cs spc2i6.gro -box 10 10 10

Output configuration contains 99678 atoms in 33226 residues
Volume :1000 (nm^3)
Density: 993.966 (g/l)
Number of SOL molecules:  33226

What would be the reason for this drastic differences in density? How can
I make it into 1000 (g/l) by using above command.

Thanks in advance.
Regards
Chandu


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.

  



--

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
 


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