Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file

[Mark James Abraham]

- Original Message -
From: Tsjerk Wassenaar <[EMAIL PROTECTED]>
Date: Saturday, February 16, 2008 6:03 pm
Subject: Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp 
file
To: Discussion list for GROMACS users 

> Hi,
> 
> grompp allows you to write the (cpp) processed topology (-pp). Since
> many parameters are controlled using cpp #define statements, cpp has
> to be called to fill the values. pdb2gmx can't do that.

The OP wanted a tool to do more than #include, they also wanted something to 
perform mapping of interaction functions from atom numbers to atom types to 
parameters. The only straightforward way to do this is via grompp. Either use 
gmxdump on the .tpr file resulting from grompp and parse the output (remember 
that numbering now starts at zero, whereas in the .top it starts at 1), or 
write a new output module for grompp to do what you want it to do, or write a 
new program to parse the .tpr file, since you can re-use a lot of existing code 
from mdrun which has to do the same task.

Mark

> On Feb 15, 2008 6:46 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
> > If you convert the tpr binary into a text file, it should have 
> every parameter in it I think?
> >
> >
> > - Original Message 
> > From: LeeHui <[EMAIL PROTECTED]>
> > To: gmx-users@gromacs.org
> > Sent: Friday, February 15, 2008 4:57:13 PM
> > Subject: [gmx-users] How to ask pdb2gmx to print all 
> parameters in the itp file
> >
> >
> > Dear all gmx users,
> >
> > I am converting the parameters in "itp" file into DL_POLY 
> format, and will be using it in my own version of DL-poly.
> > I was wondering if there is a way to ask pdb2gmx or some other 
> utilities in Gromacs to print all the parameters into itp, so I 
> don't have go to the database and find them out.
> >
> > eg. the default pdb2gmx generated itp have this format
> > [ angles ]
> > ;  aiajak 
> functc0c1c2c3
> > 1
> 231
> > 1
> 241
> > 1
> 251
> > 3
> 241
> >
> > instead of leaving c0, c1.. blank, I want the exact values of 
> them printed .
> >
> > Is there a way to this in Gromacs ?
> >
> >
> > Thanks,
> >
> >
> > Hui
> > _
> > Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！
> > http://get.live.cn/product/photo.html
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> >
> >   
> >
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> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623> ___
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Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file

[Tsjerk Wassenaar]

Hi,

grompp allows you to write the (cpp) processed topology (-pp). Since
many parameters are controlled using cpp #define statements, cpp has
to be called to fill the values. pdb2gmx can't do that.

Cheers,

Tsjerk

On Feb 15, 2008 6:46 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
> If you convert the tpr binary into a text file, it should have every 
> parameter in it I think?
>
>
> - Original Message 
> From: LeeHui <[EMAIL PROTECTED]>
> To: gmx-users@gromacs.org
> Sent: Friday, February 15, 2008 4:57:13 PM
> Subject: [gmx-users] How to ask pdb2gmx to print all parameters in the itp 
> file
>
>
> Dear all gmx users,
>
> I am converting the parameters in "itp" file into DL_POLY format, and will be 
> using it in my own version of DL-poly.
> I was wondering if there is a way to ask pdb2gmx or some other utilities in 
> Gromacs to print all the parameters into itp, so I don't have go to the 
> database and find them out.
>
> eg. the default pdb2gmx generated itp have this format
> [ angles ]
> ;  aiajak functc0c1c2
> c3
> 1231
> 1241
> 1251
> 3241
>
> instead of leaving c0, c1.. blank, I want the exact values of them printed .
>
> Is there a way to this in Gromacs ?
>
>
> Thanks,
>
>
> Hui
> _
> Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！
> http://get.live.cn/product/photo.html
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>
>
>   
> 
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] abnormal RMSD

[Tsjerk Wassenaar]

Hi,

You may have written only a subset of atoms to the new trajectory
files using trjconv. Keep track of what you're doing and what is in
which file. Besides, most analysis tools also accept .pdb/.gro files
for reference.

Cheers,

Tsjerk

On Feb 15, 2008 6:31 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
> >
> > " Molecule in topology has atom numbers below and above natoms. you are
> > probably trying to use a trajectory which does not match the first 330 atoms
> > of the run input file. You can make a matching run input file with tpbconv."
>
> Use the same .tpr file that you submitted to mdrun to generate the trajectory.
> It has the reference structure for your simulation (t=0).  Try with -pbc 
> nojump
> and -pbc whole to see which reconstructs your system appropriately.
>
> -Justin
>
> >
> > with regards
> >  Anamika
> >
>
>
>
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> 
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] eigenvalues as a function of time

[L. Michel Espinoza-Fonseca]

Hi Tsjerk,

Indeed it does make sense! Thanks for you comments.

Cheers,
Michel

PS. After all it wasn't a waste of time, isn't it? :)

On Feb 15, 2008 4:53 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Michel,
>
> Mind the eigenvectors! If you want to know how the eigenvalues
> converge, you also have to take the convergence of your eigenvectors
> into account. It may well be that for one subtrajectory one
> eigenvector is dominant, but that for a longer subtrajectory another
> is getting more important. Now, in fact any decomposition is as good
> as any other, so your best estimate for the eigenvectors to look along
> is the set obtained from the total covariance analysis. You then
> probably want to look at the convergence of the eigenvalues along
> these modes, which are basically the variances of the projections on
> these modes. In that case, you're best bet is likely to calculate the
> variances of the projections for each subtrajectory with respect to
> the corresponding average projections. The average projections all
> converge to 0, by definition and the variances will thus converge to
> the eigenvalues.
>
> O yes, this saves you quite a bit of time constructing and
> diagonalizing covariance matrices.
>
> I hope this makes sense to you :)
>
> Best,
>
> Tsjerk
>
> On Fri, Feb 15, 2008 at 7:23 AM, L. Michel Espinoza-Fonseca
>
> <[EMAIL PROTECTED]> wrote:
> > Hi Tsjerk,
> >
> >  You are right. I think that by either lack of caffeine or attention
> >  (most probably the second one) I wrote the intervals in a wrong way. I
> >  just realized it now thanks to your email. So, going back to my
> >  original post, I want to obtain the eigenvalues vs time, so then I can
> >  use them to calculate the entropy of a X system using the
> >  quasi-harmonic approximation. What I realized (if I'm correct this
> >  time) is that I need to calculate the covariance matrix *not* from
> >  isolated intervals (such as 0-500, 501-1000, etc.) but from intervals
> >  starting from the reference structure (0-500, 0-1000, 0-1500, etc.).
> >  The goal is simply to determine to what extend the entropy converges
> >  in the simulation, as it has been shown that relatively long
> >  simulations are needed for this term to converge.
> >
> >  On the other hand, splitting wasn't the right word, after all. Even
> >  now I can't find the right word. I slipped up twice.
> >
> >  I apologize for my mistake -I basically took from you a few minutes
> >  because of my lack of clarity :)
> >
> >  Cheers,
> >  Michel
> >
> >
> >
> >  On Thu, Feb 14, 2008 at 11:47 PM, Tsjerk Wassenaar <[EMAIL PROTECTED]> 
> > wrote:
> >  > Hi Michel,
> >  >
> >  >  You're principal components will be heavily undersampled (and
> >  >  therefore underdetermined), most notably the higher ones. You're
> >  >  likely not even to have more than a single uncorrelated observation
> >  >  per subtrajectory. The eigenvalue is a measure of the fluctuation, or
> >  >  actually the spread, over time. It's not that trivial to split that.
> >  >  Also note that we usually neglect the fact that we have too few
> >  >  independent observations in a trajectory as it is. You're just making
> >  >  things worse.
> >  >
> >  >  Cheers,
> >  >
> >  >  Tsjerk
> >  >
> >  >
> >  >
> >  >  On Thu, Feb 14, 2008 at 11:33 PM, L. Michel Espinoza-Fonseca
> >  >  <[EMAIL PROTECTED]> wrote:
> >  >  > Mark,
> >  >  >
> >  >  >  I have one more question. For example, if I have a trajectory of 10 
> > ns
> >  >  >  divided in intervals of 10 ps each, to obtain a set of eigenvalues
> >  >  >  each 500 ps I have to calculate the eigenvalues using the following
> >  >  >  intervals:
> >  >  >
> >  >  >  0-500 ps
> >  >  >  501-1000 ps
> >  >  >  1001-1500 ps
> >  >  >  
> >  >  >  9501-1 ps
> >  >  >
> >  >  >  Is that correct?
> >  >  >
> >  >  >  Thanks!
> >  >  >
> >  >  > Michel
> >  >  >
> >  >  >  On Thu, Feb 14, 2008 at 2:54 AM, Marcus Kubitzki <[EMAIL PROTECTED]> 
> > wrote:
> >  >  >
> >  >  >
> >  >  > > Hi Michel,
> >  >  >  >
> >  >  >  >  I'm confused by what you mean by "splitting" the eigenvalues.
> >  >  >  >  With g_covar -b -e you can get eigenvals for a specified interval 
> > of
> >  >  >  >  time, e.g. 0-1ns. Getting eigenvals as a function of time (if 
> > that's
> >  >  >  >  what I suspect you want to do), you need to run g_covar for all
> >  >  >  >  intervals 0-t1, 0-t2, 0-t3, ... to get the desired sequence.
> >  >  >  >
> >  >  >  >  Marcus
> >  >  >  >
> >  >  >  >
> >  >  >  >
> >  >  >  >
> >  >  >  >  L. Michel Espinoza-Fonseca wrote:
> >  >  >  >  > Hi all,
> >  >  >  >  >
> >  >  >  >  > I have a MD trajectory and want to split the eigenvalues as a 
> > function
> >  >  >  >  > of time. I've been trying to do so with g_covar but with no 
> > success.
> >  >  >  >  > I'd like to know if you could guide me on this matter. I'm 
> > planning to
> >  >  >  >  > further used those values to calculate the entropy (By using 
> > Karplus'
> >  >  >  >  >

[gmx-users] Stanford workshop april 7-8

[Erik Lindahl]

Hi again,

Quick update:

I've finally settled the block room reservations at the guest house  
($89 for singles, $119 for doubles), and will try to put up a  
registration page in a couple of hours.


I think I have a solution to keep it reasonably fair just in case  
there's overwhelming interest:


In the first round I'll simply let everybody register until tuesday  
night (PST) next week, and if by then there are more people than slots  
(~30) we will have to draw randomly, but give people from US/Canada/ 
Mexico priority.  Hopefully Europeans will get another chance in  
Göttingen soon :-)


From wednesday any possible remaining slots will be filled on a first- 
come, first-served, basis.


Cheers,

Erik


Erik Lindahl   <[EMAIL PROTECTED]>  Backup: <[EMAIL PROTECTED]>
Assistant Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675  Mobile: +46(0)704218767  Fax: mail a PDF instead




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[gmx-users] "rmsd distance" and "rmsd deviation" option for the -dista option of g_cluster

[OZGE ENGIN]

Hi all,

There are two options for the -dista option of the g_cluster: rmsd of distance 
and RMS deviation.
What is the difference between these two?
One of them gives the absolute rmsd of each frame and the other gives the 
relative rmsd according to the average rmsd?

Thank you

Ozge Engin
=
Computational Science & Engineering
Koc University
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Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file

[Alan Dodd]

If you convert the tpr binary into a text file, it should have every parameter 
in it I think?

- Original Message 
From: LeeHui <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Friday, February 15, 2008 4:57:13 PM
Subject: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file


Dear all gmx users, 

I am converting the parameters in "itp" file into DL_POLY format, and will be 
using it in my own version of DL-poly. 
I was wondering if there is a way to ask pdb2gmx or some other utilities in 
Gromacs to print all the parameters into itp, so I don't have go to the 
database and find them out. 

eg. the default pdb2gmx generated itp have this format 
[ angles ]
;  aiajak functc0c1c2c3
1231
1241
1251
3241

instead of leaving c0, c1.. blank, I want the exact values of them printed . 

Is there a way to this in Gromacs ?


Thanks, 


Hui 
_
Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！
http://get.live.cn/product/photo.html
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Find them fast with Yahoo! Search.  
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Re: [gmx-users] abnormal RMSD

[Justin A. Lemkul]

>
> " Molecule in topology has atom numbers below and above natoms. you are
> probably trying to use a trajectory which does not match the first 330 atoms
> of the run input file. You can make a matching run input file with tpbconv."

Use the same .tpr file that you submitted to mdrun to generate the trajectory. 
It has the reference structure for your simulation (t=0).  Try with -pbc nojump
and -pbc whole to see which reconstructs your system appropriately.

-Justin

>
> with regards
>  Anamika
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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[gmx-users] How to ask pdb2gmx to print all parameters in the itp file

[LeeHui]

Dear all gmx users, 

I am converting the parameters in "itp" file into DL_POLY format, and will be 
using it in my own version of DL-poly. 
I was wondering if there is a way to ask pdb2gmx or some other utilities in 
Gromacs to print all the parameters into itp, so I don't have go to the 
database and find them out. 

eg. the default pdb2gmx generated itp have this format 
[ angles ]
;  aiajak functc0c1c2c3
1 2 3 1
1 2 4 1
1 2 5 1
3 2 4 1

instead of leaving c0, c1.. blank, I want the exact values of them printed . 

Is there a way to this in Gromacs ?


Thanks, 


Hui 
_
Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！
http://get.live.cn/product/photo.html
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[gmx-users] Abnormal RMSD

[Anamika Awasthi]

Dear all,
 Thanks Florian and Justin for your suggestions
  I am an beginner, so I am writing all the commands which I used
 pdb2gmx -f *.pdb -o *.gro -p *.top
then
editconf -f *.gro -o *out.gro -c -d 0.8

genbox -cp *out.gro -cs -o *b4ion.gro -p *.top

grompp -f em.mdp -po *out.mdp -c *b4ion.gro -p *.top -o *b4ion.tpr

neutralized system

genion -s *b4ion.tpr -o *b4em.gro -pname Na -np 10 -g *ion.log

select group 12

editing in *.top file

grompp -f em.mdp -c *b4em.gro -p *.top -o *em.tpr

mdrun -s *em.tpr -o *em.trr -c *b4pr.gro -g em.log -e em.edr

grompp -f pr.mdp -c *b4pr.gro -p *.top -o *pr.tpr

mdrun -s *pr.tpr -o *pr.trr -c *b4md.gro -g pr.log -e pr.edr

grompp -f md.mdp -c *b4md.gro -p *.top -o *md.tpr

mdrun -s *md.tpr -o *md.trr -c *pmd.gro -g md.log -e md.edr

HOPE this will help to understand my problem

 with regards
 Anamika
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Re: [gmx-users] problem regarding insertion of protein into lipidbilayer

[Stéphane Téletchéa]

Justin A. Lemkul a écrit :

Quoting sudheer babu <[EMAIL PROTECTED]>:


hi gmx users,
i am new to gromacs , i am doing membrane protein simulations. My popc
bilayer contain 128 molecules and protein contain 59 aminoacid residues,
both systems i have simulated for 1ns . Now i want insert my protein into
membrane. I have searched alot in gmxusers for how to insert protein into
membrane and found that some are used make_hole.pl program, some of them
have used genbox insertion command,
The above mentioned two ways which one i have to follow,  can anyone tell
detail information.
Thanks in advance.



Either one should work, just be aware that make_hole.pl was designed for an
older version of Gromacs (3.1? 3.2?), and I believe some difficulties have been
reported when using it with Gromacs version 3.3.x.

To use genbox is trivial; orient your protein appropriately and use your POPC
structure as -cs input.  There have been lots of discussion about how to do
this and the problems people have faced.  No doubt you have seen these, since
you have been searching the archive :-)

-Justin


Consider also inflategro.pl and its accompanying paper, you'll save a 
lot of time in the beginning.


Both info at http://moose.bio.ucalgary.ca/index.php?page=Programs

Cheers,
Stéphane

--
Stéphane Téletchéa, PhD.  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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[gmx-users] abnormal RMSD

[Anamika Awasthi]

Thankyou Justin for your suggestion

I tried this command--->

trjconv -f myprotein.trr -o trajout_whole.trr -pbc  whole

 this was showing this error

 "can not open file
   topol.tpr"
 then
I repeated the same command with "-s topol.tpr"

then

trjconv -f trajout_whole.trr -o trajout_nojump.trr -pbc nojump

then

g_rms -s topol.tpr -f trajout_nojump.trr -o trajout_nojump_rmsd.xvg -xvgr

but now this is showing Fatal Error

" Molecule in topology has atom numbers below and above natoms. you are
probably trying to use a trajectory which does not match the first 330 atoms
of the run input file. You can make a matching run input file with tpbconv."

with regards
 Anamika
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Re: [gmx-users] problem regarding insertion of protein into lipidbilayer

[Justin A. Lemkul]

Quoting sudheer babu <[EMAIL PROTECTED]>:

> hi gmx users,
> i am new to gromacs , i am doing membrane protein simulations. My popc
> bilayer contain 128 molecules and protein contain 59 aminoacid residues,
> both systems i have simulated for 1ns . Now i want insert my protein into
> membrane. I have searched alot in gmxusers for how to insert protein into
> membrane and found that some are used make_hole.pl program, some of them
> have used genbox insertion command,
> The above mentioned two ways which one i have to follow,  can anyone tell
> detail information.
> Thanks in advance.
>

Either one should work, just be aware that make_hole.pl was designed for an
older version of Gromacs (3.1? 3.2?), and I believe some difficulties have been
reported when using it with Gromacs version 3.3.x.

To use genbox is trivial; orient your protein appropriately and use your POPC
structure as -cs input.  There have been lots of discussion about how to do
this and the problems people have faced.  No doubt you have seen these, since
you have been searching the archive :-)

-Justin




Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] toluene tutorial sc-power value

[Maik Goette]

Fine :)
So forget what I wrote before...I mentioned exactly that :)

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


[EMAIL PROTECTED] wrote:

Hi maik
I made the calculation with sc-power=2 adding 3 lambda values. Now i get
integrating the plot of average free energy for the mutation of toluene in
water 0.559 instead of 15,8 in previous calculation.
if i combine with the free energy in vacuo i have -3,41 KJ/mol vs (-3,1
KJ/mol exp.). This is quite ok!! :)
So the error was a combination of number of points- sc-parameter but for
sure number of points are really important for the integration part!!! in
the calculation of free energy.
. regards
geraldine


On Fri, February 15, 2008 11:07 am, Maik Goette wrote:

I had a veeery short look into the tutorial and found an error.


DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong.


The correct cycle would be:


DG_1+DG_3=DG_hyd+DG_2


=>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0


So its:
DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3


Anyway, this won't help you, cause the only effect is a change of the
sign to +19 and therefore worse.

Can you show me the topology, you made?
As far as the free energy experts here discussed it, sc-power=2
shouldn't be the lambda-dependance of choice. I can agree to that from my
simulations.

regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/



[EMAIL PROTECTED] wrote:

Hi maik


the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water)


for fisrt one deltaG_mutation(vacuo) =-2,85 for second
deltaGmutation(water) =15,87

so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol

i'll do a series of calculation with sc-power=2 and see the difference
see if there's some significant difference. geraldine


On Thu, February 14, 2008 10:57 am, Maik Goette wrote:


Hi



Now, make sure, that you apply the thermodynamic cycle correctly.
I wouldn't wonder about large errors. Depending on the definition of
large. Error estimation from free energy calculations can be very
tricky. Using mpi shouldn't influence your calculations outcome.
Still I don't know the error.
How to post the numbers: Exp. value (+error) and your calculated value
 (+error) ? From those I could tell you if something is terribly
wrong or not. :)

Regards



Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de WWW   :
http://www.mpibpc.gwdg.de/groups/grubmueller/




[EMAIL PROTECTED] wrote:

Hi MaiK,
Sorry i forgot the subject. Thank you to have answered this email.
This
tutorial is about solvation free energy of toluene using
thermodynamical cycles. two energies have to be calculated according
to this cycle, the hydration energy of toluene and the mutation
energy from dummy to toluene in vacuo. For each energy calculation
several MD simulation for different lambda value must be performed.
in the mdp files given i added the line sc-power=1 and made the
calculation. from the file dgdl.xvg obtained for each lambda value i
used the g_analyse command to get the average and the estimated
error of free energy. i made the plot =f(lambda) for the first
part (hydration of toluene) integrated and get the integrated value
of the plot and did the same for mutation energy of toluene and made
the difference of the two integrated values. I really don't know
where the error came from : -version of gromacs, the fact that mpi
has been used for the first part and single process for the mutation
part (because of shake block problem) won't change anything i guess,
I would carefully go through one
more time and check why i didn't get the right value. I don't know
if this high estimated   error is really problematic. regards
geraldine

On Wed, February 13, 2008 6:19 pm, Maik Goette wrote:



Hi




First of all: You can be quite happy, if anyone reads a "no
subject" mail. sc-power seems to be set to zero in the newer
version, in contrast to the old ones, where it was 1 by default.
Therefore GROMACS
complains. 1 is the value, you should use. I don't know the
tutorial, but if you use exactly the files given there (and add
sc-power = 1), you should get values, which are close to the
experimental one (I guess, cause a tutorial won't make sense, if
the files don't yield the desired value).

Sorry, but more help is hard to give with 

Re: [gmx-users] toluene tutorial sc-power value

[Maik Goette]

hi

10 points is strange ;)
11 is the number with equally spaced points. ANyway, it should suffice 
to get a more or less proper number.
I guess, they use simpsons integration, what should be ok. I compared my 
scripts results, which uses simpson, with those of xmgrace and they fit.
The longer you sample each lambda value and the more lambda values you 
sample, the better the results, but with this system, I think, 11 lambda 
values with 1ns each should be enough.
Be aware of the fact, that you should cut away a few picoseconds of each 
dgdl-file for equilibration purposes (100-200).


The topology seems not too bad. I'm not used to that forcefield, though.

As a general suggestion, its always better to sample many lambda points 
and each longer, than wasting time with using sc-power=2 :)


Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


[EMAIL PROTECTED] wrote:

hi

concerning the cycle i saw this error since i started the tutorial, i paid
attention to that but as you said it's not that important since my energy
value is too high. i'm right now doing the problem again with sc-power=2
and also 10 points is it enough to have an approximate correct value since
i have to integrate the average energy plot by xmgrace, i don't know what
kind of integration they use, trapezoid? or... it could have an effect if
i don't have enough point. but then .. here attached is my top. file.
regards
geraldine







On Fri, February 15, 2008 11:07 am, Maik Goette wrote:

I had a veeery short look into the tutorial and found an error.


DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong.


The correct cycle would be:


DG_1+DG_3=DG_hyd+DG_2


=>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0


So its:
DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3


Anyway, this won't help you, cause the only effect is a change of the
sign to +19 and therefore worse.

Can you show me the topology, you made?
As far as the free energy experts here discussed it, sc-power=2
shouldn't be the lambda-dependance of choice. I can agree to that from my
simulations.

regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/



[EMAIL PROTECTED] wrote:

Hi maik


the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water)


for fisrt one deltaG_mutation(vacuo) =-2,85 for second
deltaGmutation(water) =15,87

so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol

i'll do a series of calculation with sc-power=2 and see the difference
see if there's some significant difference. geraldine


On Thu, February 14, 2008 10:57 am, Maik Goette wrote:


Hi



Now, make sure, that you apply the thermodynamic cycle correctly.
I wouldn't wonder about large errors. Depending on the definition of
large. Error estimation from free energy calculations can be very
tricky. Using mpi shouldn't influence your calculations outcome.
Still I don't know the error.
How to post the numbers: Exp. value (+error) and your calculated value
 (+error) ? From those I could tell you if something is terribly
wrong or not. :)

Regards



Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de WWW   :
http://www.mpibpc.gwdg.de/groups/grubmueller/




[EMAIL PROTECTED] wrote:

Hi MaiK,
Sorry i forgot the subject. Thank you to have answered this email.
This
tutorial is about solvation free energy of toluene using
thermodynamical cycles. two energies have to be calculated according
to this cycle, the hydration energy of toluene and the mutation
energy from dummy to toluene in vacuo. For each energy calculation
several MD simulation for different lambda value must be performed.
in the mdp files given i added the line sc-power=1 and made the
calculation. from the file dgdl.xvg obtained for each lambda value i
used the g_analyse command to get the average and the estimated
error of free energy. i made the plot =f(lambda) for the first
part (hydration of toluene) integrated and get the integrated value
of the plot and did the same for mutation energy of toluene and made
the difference of the two integrated values. I really don't know
where the error came from : -version of gromacs, the fact that mpi
has been used for the first part and single process for the mutation
part (because of shake block problem) won't change anything i guess,
I would care

[gmx-users] problem regarding insertion of protein into lipidbilayer

[sudheer babu]

hi gmx users,
i am new to gromacs , i am doing membrane protein simulations. My popc
bilayer contain 128 molecules and protein contain 59 aminoacid residues,
both systems i have simulated for 1ns . Now i want insert my protein into
membrane. I have searched alot in gmxusers for how to insert protein into
membrane and found that some are used make_hole.pl program, some of them
have used genbox insertion command,
The above mentioned two ways which one i have to follow,  can anyone tell
detail information.
Thanks in advance.
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Re: [gmx-users] Abnormal fluctuation in RMSD

[Justin A. Lemkul]

Quoting Anamika Awasthi <[EMAIL PROTECTED]>:

>  Dear all,
>
> I am working on a biological dimer of 330 residues.
> I dont think that I got any error message when I did grompp.

Don't think, or don't know?  These types of things are important.

> Please find pr.mdp filesbelow and RMSD as attachment.
> Please tell me why it happened?

Well, look at your trajectory - what's happening when the RMSD graph spikes? 
That should provide you with some ideas.  My guess would be your protein is
jumping across the simulation box, but you have not described your setup - box
size/distance from protein to the box edge, and whether or not you observed any
periodic jumping.

-Justin

>
> pr.mdp
> ;
> ;   User spoel (236)
> ;   Wed Nov  3 17:12:44 1993
> ;   Input file
> title   =   CM_2ao2_A
> cpp =  /usr/bin/cpp
> define  =  -DPOSRES
> constraints =  all-bonds
> integrator  =  md
> dt  =  0.001
> nsteps  =  10
> nstcomm =  1
> nstxout =  250
> nstvout =  1000
> nstfout =  0
> nstlog  =  10
> nstlist =  10
> ns_type =  grid
> rlist   =  1
> coulombtype =  PME
> rcoulomb=  1.0
> rvdw=  1.0
> fourierspacing  =  0.12
> fourier_nx  =  0
> fourier_ny  =  0
> fourier_nz  =  0
> pme_order   =  4
> ewald_rtol  =  1e-5
> optimize_fft=  yes
> ;
> ; Berendsen temperature coupling is on
> Tcoupl  = berendsen
> tau_t   = 0.01  0.01
> tc_grps = protein   non-protein
> ref_t   = 300   300
> ; Pressure coupling is on
> Pcoupl  =  berendsen
> pcoupltype =  isotropic
> tau_p   =  0.5
> compressibility =  4.5e-5
> ref_p   =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel =  yes
> gen_temp= 300.0
> gen_seed= 173529
>
>
> Thanking you
>
>  With best regards
>  Anamika
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] Abnormal fluctuation in RMSD

[Florian Haberl]

Hi,

On Friday, 15. February 2008 14:51, Anamika Awasthi wrote:
>  Dear all,
>
> I am working on a biological dimer of 330 residues.
> I dont think that I got any error message when I did grompp.
> Please find pr.mdp filesbelow and RMSD as attachment.
> Please tell me why it happened?
>
> pr.mdp
> ;
> ;   User spoel (236)
> ;   Wed Nov  3 17:12:44 1993
> ;   Input file
> title   =   CM_2ao2_A
> cpp =  /usr/bin/cpp
> define  =  -DPOSRES
> constraints =  all-bonds
> integrator  =  md
> dt  =  0.001
> nsteps  =  10
> nstcomm =  1
> nstxout =  250
> nstvout =  1000
> nstfout =  0
> nstlog  =  10
> nstlist =  10
> ns_type =  grid
> rlist   =  1
> coulombtype =  PME
> rcoulomb=  1.0
> rvdw=  1.0
> fourierspacing  =  0.12
> fourier_nx  =  0
> fourier_ny  =  0
> fourier_nz  =  0
> pme_order   =  4
> ewald_rtol  =  1e-5
> optimize_fft=  yes
> ;
> ; Berendsen temperature coupling is on
> Tcoupl  = berendsen
> tau_t   = 0.01  0.01
> tc_grps = protein   non-protein
> ref_t   = 300   300
> ; Pressure coupling is on
> Pcoupl  =  berendsen
> pcoupltype =  isotropic
> tau_p   =  0.5
> compressibility =  4.5e-5
> ref_p   =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel =  yes
> gen_temp= 300.0
> gen_seed= 173529
>
>
> Thanking you
>
>  With best regards
>  Anamika

you are using PBC and your system is sometimes jumping out of the box, so you 
have to mirror it back to its normal box


trjconv -f yourtraj.trr -o yourtraj_fit.trr -s topol.tpr -pbc nojump

should fix it again.


Greetings,

Florian

-- 
---
 Florian Haberl
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
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Re: [gmx-users] toluene tutorial sc-power value

[cilpa]

Hi maik
I made the calculation with sc-power=2 adding 3 lambda values. Now i get
integrating the plot of average free energy for the mutation of toluene in
water 0.559 instead of 15,8 in previous calculation.
if i combine with the free energy in vacuo i have -3,41 KJ/mol vs (-3,1
KJ/mol exp.). This is quite ok!! :)
So the error was a combination of number of points- sc-parameter but for
sure number of points are really important for the integration part!!! in
the calculation of free energy.
. regards
geraldine


On Fri, February 15, 2008 11:07 am, Maik Goette wrote:
> I had a veeery short look into the tutorial and found an error.
>
>
> DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong.
>
>
> The correct cycle would be:
>
>
> DG_1+DG_3=DG_hyd+DG_2
>
>
> =>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0
>
>
> So its:
> DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3
>
>
> Anyway, this won't help you, cause the only effect is a change of the
> sign to +19 and therefore worse.
>
> Can you show me the topology, you made?
> As far as the free energy experts here discussed it, sc-power=2
> shouldn't be the lambda-dependance of choice. I can agree to that from my
> simulations.
>
> regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> mgoette2[at]gwdg.de WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
>
> [EMAIL PROTECTED] wrote:
>> Hi maik
>>
>>
>> the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water)
>>
>>
>> for fisrt one deltaG_mutation(vacuo) =-2,85 for second
>> deltaGmutation(water) =15,87
>>
>> so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol
>>
>> i'll do a series of calculation with sc-power=2 and see the difference
>> see if there's some significant difference. geraldine
>>
>>
>> On Thu, February 14, 2008 10:57 am, Maik Goette wrote:
>>
>>> Hi
>>>
>>>
>>>
>>> Now, make sure, that you apply the thermodynamic cycle correctly.
>>> I wouldn't wonder about large errors. Depending on the definition of
>>> large. Error estimation from free energy calculations can be very
>>> tricky. Using mpi shouldn't influence your calculations outcome.
>>> Still I don't know the error.
>>> How to post the numbers: Exp. value (+error) and your calculated value
>>>  (+error) ? From those I could tell you if something is terribly
>>> wrong or not. :)
>>>
>>> Regards
>>>
>>>
>>>
>>> Maik Goette, Dipl. Biol.
>>> Max Planck Institute for Biophysical Chemistry
>>> Theoretical & computational biophysics department
>>> Am Fassberg 11
>>> 37077 Goettingen
>>> Germany
>>> Tel.  : ++49 551 201 2310
>>> Fax   : ++49 551 201 2302
>>> Email : mgoette[at]mpi-bpc.mpg.de
>>> mgoette2[at]gwdg.de WWW   :
>>> http://www.mpibpc.gwdg.de/groups/grubmueller/
>>>
>>>
>>>
>>>
>>> [EMAIL PROTECTED] wrote:
 Hi MaiK,
 Sorry i forgot the subject. Thank you to have answered this email.
 This
 tutorial is about solvation free energy of toluene using
 thermodynamical cycles. two energies have to be calculated according
 to this cycle, the hydration energy of toluene and the mutation
 energy from dummy to toluene in vacuo. For each energy calculation
 several MD simulation for different lambda value must be performed.
 in the mdp files given i added the line sc-power=1 and made the
 calculation. from the file dgdl.xvg obtained for each lambda value i
 used the g_analyse command to get the average and the estimated
 error of free energy. i made the plot =f(lambda) for the first
 part (hydration of toluene) integrated and get the integrated value
 of the plot and did the same for mutation energy of toluene and made
 the difference of the two integrated values. I really don't know
 where the error came from : -version of gromacs, the fact that mpi
 has been used for the first part and single process for the mutation
 part (because of shake block problem) won't change anything i guess,
 I would carefully go through one
 more time and check why i didn't get the right value. I don't know
 if this high estimated   error is really problematic. regards
 geraldine

 On Wed, February 13, 2008 6:19 pm, Maik Goette wrote:


> Hi
>
>
>
>
> First of all: You can be quite happy, if anyone reads a "no
> subject" mail. sc-power seems to be set to zero in the newer
> version, in contrast to the old ones, where it was 1 by default.
> Therefore GROMACS
> complains. 1 is the value, you should use. I don't know the
> tutorial, but if you use exactly the files given there (and add
> sc-power = 1), you should get values, which are close to the
> experimental one (I guess, cause a tutorial won't make sense, if
> the files don't yield the desired value).
>
> Sorry, but more help is ha

[gmx-users] Abnormal fluctuation in RMSD

[Anamika Awasthi]

 Dear all,

I am working on a biological dimer of 330 residues.
I dont think that I got any error message when I did grompp.
Please find pr.mdp filesbelow and RMSD as attachment.
Please tell me why it happened?

pr.mdp
;
;   User spoel (236)
;   Wed Nov  3 17:12:44 1993
;   Input file
title   =   CM_2ao2_A
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.001
nsteps  =  10
nstcomm =  1
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstlist =  10
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb=  1.0
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
;
; Berendsen temperature coupling is on
Tcoupl  = berendsen
tau_t   = 0.01  0.01
tc_grps = protein   non-protein
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  =  berendsen
pcoupltype =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp= 300.0
gen_seed= 173529


Thanking you

 With best regards
 Anamika
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Re: [gmx-users] there is no enough information about the implementation of both diagonalization and Monte Carlo methods of g_cluster in the manual

[David van der Spoel]

OZGE ENGIN wrote:

Hi all,

I have two questions about the g_cluster.

1)
I want to test the performance of the clustering methods implemented in g_cluster. However, although there are some information about the gromos,Jarvis Patrick, and single linkage methods both in the manual and on the internet, there are no information about the implementation of both the Monte Carlo and the diagonalization method. 

I know that when diagonalizing a matrix, the eigenvalues are found, and then how they are used for the clustering? 

use the source. this is not a published or very well tested method. so 
please be careful when using it.




2)There are two options for the -dista option of the g_cluster: rmsd of 
distance and RMS deviation. What is the difference between these two?
One of them gives the absolute rmsd of each frame and the other gives the 
relative rmsd according to the average rmsd?

Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] there is no enough information about the implementation of both diagonalization and Monte Carlo methods of g_cluster in the manual

[OZGE ENGIN]

Hi all,

I have two questions about the g_cluster.

1)
I want to test the performance of the clustering methods implemented in 
g_cluster. However, although there are some information about the gromos,Jarvis 
Patrick, and single linkage methods both in the manual and on the internet, 
there are no information about the implementation of both the Monte Carlo and 
the diagonalization method.

I know that when diagonalizing a matrix, the eigenvalues are found, and then 
how they are used for the clustering?

2)There are two options for the -dista option of the g_cluster: rmsd of 
distance and RMS deviation. What is the difference between these two?
One of them gives the absolute rmsd of each frame and the other gives the 
relative rmsd according to the average rmsd?

Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
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Re: [gmx-users] toluene tutorial sc-power value

[cilpa]

hi

concerning the cycle i saw this error since i started the tutorial, i paid
attention to that but as you said it's not that important since my energy
value is too high. i'm right now doing the problem again with sc-power=2
and also 10 points is it enough to have an approximate correct value since
i have to integrate the average energy plot by xmgrace, i don't know what
kind of integration they use, trapezoid? or... it could have an effect if
i don't have enough point. but then .. here attached is my top. file.
regards
geraldine







On Fri, February 15, 2008 11:07 am, Maik Goette wrote:
> I had a veeery short look into the tutorial and found an error.
>
>
> DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong.
>
>
> The correct cycle would be:
>
>
> DG_1+DG_3=DG_hyd+DG_2
>
>
> =>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0
>
>
> So its:
> DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3
>
>
> Anyway, this won't help you, cause the only effect is a change of the
> sign to +19 and therefore worse.
>
> Can you show me the topology, you made?
> As far as the free energy experts here discussed it, sc-power=2
> shouldn't be the lambda-dependance of choice. I can agree to that from my
> simulations.
>
> regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> mgoette2[at]gwdg.de WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
>
> [EMAIL PROTECTED] wrote:
>> Hi maik
>>
>>
>> the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water)
>>
>>
>> for fisrt one deltaG_mutation(vacuo) =-2,85 for second
>> deltaGmutation(water) =15,87
>>
>> so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol
>>
>> i'll do a series of calculation with sc-power=2 and see the difference
>> see if there's some significant difference. geraldine
>>
>>
>> On Thu, February 14, 2008 10:57 am, Maik Goette wrote:
>>
>>> Hi
>>>
>>>
>>>
>>> Now, make sure, that you apply the thermodynamic cycle correctly.
>>> I wouldn't wonder about large errors. Depending on the definition of
>>> large. Error estimation from free energy calculations can be very
>>> tricky. Using mpi shouldn't influence your calculations outcome.
>>> Still I don't know the error.
>>> How to post the numbers: Exp. value (+error) and your calculated value
>>>  (+error) ? From those I could tell you if something is terribly
>>> wrong or not. :)
>>>
>>> Regards
>>>
>>>
>>>
>>> Maik Goette, Dipl. Biol.
>>> Max Planck Institute for Biophysical Chemistry
>>> Theoretical & computational biophysics department
>>> Am Fassberg 11
>>> 37077 Goettingen
>>> Germany
>>> Tel.  : ++49 551 201 2310
>>> Fax   : ++49 551 201 2302
>>> Email : mgoette[at]mpi-bpc.mpg.de
>>> mgoette2[at]gwdg.de WWW   :
>>> http://www.mpibpc.gwdg.de/groups/grubmueller/
>>>
>>>
>>>
>>>
>>> [EMAIL PROTECTED] wrote:
 Hi MaiK,
 Sorry i forgot the subject. Thank you to have answered this email.
 This
 tutorial is about solvation free energy of toluene using
 thermodynamical cycles. two energies have to be calculated according
 to this cycle, the hydration energy of toluene and the mutation
 energy from dummy to toluene in vacuo. For each energy calculation
 several MD simulation for different lambda value must be performed.
 in the mdp files given i added the line sc-power=1 and made the
 calculation. from the file dgdl.xvg obtained for each lambda value i
 used the g_analyse command to get the average and the estimated
 error of free energy. i made the plot =f(lambda) for the first
 part (hydration of toluene) integrated and get the integrated value
 of the plot and did the same for mutation energy of toluene and made
 the difference of the two integrated values. I really don't know
 where the error came from : -version of gromacs, the fact that mpi
 has been used for the first part and single process for the mutation
 part (because of shake block problem) won't change anything i guess,
 I would carefully go through one
 more time and check why i didn't get the right value. I don't know
 if this high estimated   error is really problematic. regards
 geraldine

 On Wed, February 13, 2008 6:19 pm, Maik Goette wrote:


> Hi
>
>
>
>
> First of all: You can be quite happy, if anyone reads a "no
> subject" mail. sc-power seems to be set to zero in the newer
> version, in contrast to the old ones, where it was 1 by default.
> Therefore GROMACS
> complains. 1 is the value, you should use. I don't know the
> tutorial, but if you use exactly the files given there (and add
> sc-power = 1), you should get values, which are close to the
> experimental one (I guess, cause a tutorial won't make sense, if
> the files don't yield the desired value).
>
> Sorr

Re: [gmx-users] eigenvalues as a function of time

[Tsjerk Wassenaar]

Hi Michel,

Mind the eigenvectors! If you want to know how the eigenvalues
converge, you also have to take the convergence of your eigenvectors
into account. It may well be that for one subtrajectory one
eigenvector is dominant, but that for a longer subtrajectory another
is getting more important. Now, in fact any decomposition is as good
as any other, so your best estimate for the eigenvectors to look along
is the set obtained from the total covariance analysis. You then
probably want to look at the convergence of the eigenvalues along
these modes, which are basically the variances of the projections on
these modes. In that case, you're best bet is likely to calculate the
variances of the projections for each subtrajectory with respect to
the corresponding average projections. The average projections all
converge to 0, by definition and the variances will thus converge to
the eigenvalues.

O yes, this saves you quite a bit of time constructing and
diagonalizing covariance matrices.

I hope this makes sense to you :)

Best,

Tsjerk

On Fri, Feb 15, 2008 at 7:23 AM, L. Michel Espinoza-Fonseca
<[EMAIL PROTECTED]> wrote:
> Hi Tsjerk,
>
>  You are right. I think that by either lack of caffeine or attention
>  (most probably the second one) I wrote the intervals in a wrong way. I
>  just realized it now thanks to your email. So, going back to my
>  original post, I want to obtain the eigenvalues vs time, so then I can
>  use them to calculate the entropy of a X system using the
>  quasi-harmonic approximation. What I realized (if I'm correct this
>  time) is that I need to calculate the covariance matrix *not* from
>  isolated intervals (such as 0-500, 501-1000, etc.) but from intervals
>  starting from the reference structure (0-500, 0-1000, 0-1500, etc.).
>  The goal is simply to determine to what extend the entropy converges
>  in the simulation, as it has been shown that relatively long
>  simulations are needed for this term to converge.
>
>  On the other hand, splitting wasn't the right word, after all. Even
>  now I can't find the right word. I slipped up twice.
>
>  I apologize for my mistake -I basically took from you a few minutes
>  because of my lack of clarity :)
>
>  Cheers,
>  Michel
>
>
>
>  On Thu, Feb 14, 2008 at 11:47 PM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
>  > Hi Michel,
>  >
>  >  You're principal components will be heavily undersampled (and
>  >  therefore underdetermined), most notably the higher ones. You're
>  >  likely not even to have more than a single uncorrelated observation
>  >  per subtrajectory. The eigenvalue is a measure of the fluctuation, or
>  >  actually the spread, over time. It's not that trivial to split that.
>  >  Also note that we usually neglect the fact that we have too few
>  >  independent observations in a trajectory as it is. You're just making
>  >  things worse.
>  >
>  >  Cheers,
>  >
>  >  Tsjerk
>  >
>  >
>  >
>  >  On Thu, Feb 14, 2008 at 11:33 PM, L. Michel Espinoza-Fonseca
>  >  <[EMAIL PROTECTED]> wrote:
>  >  > Mark,
>  >  >
>  >  >  I have one more question. For example, if I have a trajectory of 10 ns
>  >  >  divided in intervals of 10 ps each, to obtain a set of eigenvalues
>  >  >  each 500 ps I have to calculate the eigenvalues using the following
>  >  >  intervals:
>  >  >
>  >  >  0-500 ps
>  >  >  501-1000 ps
>  >  >  1001-1500 ps
>  >  >  
>  >  >  9501-1 ps
>  >  >
>  >  >  Is that correct?
>  >  >
>  >  >  Thanks!
>  >  >
>  >  > Michel
>  >  >
>  >  >  On Thu, Feb 14, 2008 at 2:54 AM, Marcus Kubitzki <[EMAIL PROTECTED]> 
> wrote:
>  >  >
>  >  >
>  >  > > Hi Michel,
>  >  >  >
>  >  >  >  I'm confused by what you mean by "splitting" the eigenvalues.
>  >  >  >  With g_covar -b -e you can get eigenvals for a specified interval of
>  >  >  >  time, e.g. 0-1ns. Getting eigenvals as a function of time (if that's
>  >  >  >  what I suspect you want to do), you need to run g_covar for all
>  >  >  >  intervals 0-t1, 0-t2, 0-t3, ... to get the desired sequence.
>  >  >  >
>  >  >  >  Marcus
>  >  >  >
>  >  >  >
>  >  >  >
>  >  >  >
>  >  >  >  L. Michel Espinoza-Fonseca wrote:
>  >  >  >  > Hi all,
>  >  >  >  >
>  >  >  >  > I have a MD trajectory and want to split the eigenvalues as a 
> function
>  >  >  >  > of time. I've been trying to do so with g_covar but with no 
> success.
>  >  >  >  > I'd like to know if you could guide me on this matter. I'm 
> planning to
>  >  >  >  > further used those values to calculate the entropy (By using 
> Karplus'
>  >  >  >  > approximation) vs time and its convergence in the simulation.
>  >  >  >  >
>  >  >  >  > Cheers,
>  >  >  >  > Michel
>  >  >  >  > ___
>  >  >  >  > 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 lis

Re: [gmx-users] toluene tutorial sc-power value

[Maik Goette]

I had a veeery short look into the tutorial and found an error.

DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong.

The correct cycle would be:

DG_1+DG_3=DG_hyd+DG_2

=>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0

So its:
DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3

Anyway, this won't help you, cause the only effect is a change of the 
sign to +19 and therefore worse.


Can you show me the topology, you made?
As far as the free energy experts here discussed it, sc-power=2 
shouldn't be the lambda-dependance of choice.

I can agree to that from my simulations.

regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


[EMAIL PROTECTED] wrote:

Hi maik

the energy
DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water)

for fisrt one deltaG_mutation(vacuo) =-2,85
for second deltaGmutation(water) =15,87

so i found DEltaG_hyd = -19 kj/mol
instead of -3,1 kj/mol

i'll do a series of calculation with sc-power=2 and see the difference
see if there's some significant difference.
geraldine


On Thu, February 14, 2008 10:57 am, Maik Goette wrote:

Hi


Now, make sure, that you apply the thermodynamic cycle correctly.
I wouldn't wonder about large errors. Depending on the definition of
large. Error estimation from free energy calculations can be very tricky.
Using mpi shouldn't influence your calculations outcome.
Still I don't know the error.
How to post the numbers: Exp. value (+error) and your calculated value
(+error) ? From those I could tell you if something is terribly wrong or
not. :)

Regards


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/



[EMAIL PROTECTED] wrote:

Hi MaiK,
Sorry i forgot the subject. Thank you to have answered this email. This
tutorial is about solvation free energy of toluene using thermodynamical
 cycles. two energies have to be calculated according to this cycle,
the hydration energy of toluene and the mutation energy from dummy to
toluene in vacuo. For each energy calculation several MD simulation for
different lambda value must be performed. in the mdp files given i added
the line sc-power=1 and made the calculation. from the file dgdl.xvg
obtained for each lambda value i used the g_analyse command to get the
average and the estimated error of free energy. i made the plot
=f(lambda) for the first part (hydration of toluene)
integrated and get the integrated value of the plot and did the same for
 mutation energy of toluene and made the difference of the two
integrated values. I really don't know where the error came from :
-version of gromacs, the fact that mpi has been used for the first part
 and single process for the mutation part (because of shake block
problem) won't change anything i guess, I would carefully go through one
more time and check why i didn't get the right value. I don't know if
this high estimated   error is really problematic. regards geraldine

On Wed, February 13, 2008 6:19 pm, Maik Goette wrote:


Hi



First of all: You can be quite happy, if anyone reads a "no subject"
mail. sc-power seems to be set to zero in the newer version, in
contrast to the old ones, where it was 1 by default. Therefore GROMACS
complains. 1 is the value, you should use. I don't know the tutorial,
but if you use exactly the files given there (and add sc-power = 1),
you should get values, which are close to the experimental one (I
guess, cause a tutorial won't make sense, if the files don't yield the
desired value).

Sorry, but more help is hard to give with so few information.



Regards



Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de WWW   :
http://www.mpibpc.gwdg.de/groups/grubmueller/




[EMAIL PROTECTED] wrote:

Hi all,
i 'm a beginner in molecular dynamics. I was doing the tutorial of
md group, hydration free energy of toluene :
http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.h
tml


i have some problems regarding the calculation of toluene in water.
the thing is that in the examples files equ-10.00.mdp and
data-10.00.mdp no sc-power were mentioned and doing the calculation
the error files mentioned about sc-power must be >0 so i added this
line sc-power=1 to those files. Analyzing the dgdl.xvg files the
estimate error(err. est.) is about 5.79 for each lambda value
studied while the mutation of tol

Re: [gmx-users] (no subject)

[Maik Goette]

grompp cant find your mdp-file.

Please give a subject next time, as well as more detailed information.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Luisa Calvanese wrote:


Hello gmx-users,
 
when I try to generate preprocessing binary files (.tpr) using the

grompp command the following error message appears:
 


creating statusfile for 1 node...

 


---

Program grompp, VERSION 3.3.2

Source code file: futil.c, line: 345

 


File input/output error:

min0.mdp

---

 


Can you help me?

 

Luisa 

 




Messenger Giochi Prenditi una pausa e sfida i tuoi amici a Ladybird su 
Messenger! 





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[gmx-users] (no subject)

[Luisa Calvanese]

Hello gmx-users, when I try to generate preprocessing binary files (.tpr) using 
the grompp command the following error message appears: 
creating statusfile for 1 node...
 
---
Program grompp, VERSION 3.3.2
Source code file: futil.c, line: 345
 
File input/output error:
min0.mdp
---
 
Can you help me?
 
Luisa  
_
Scarica GRATIS le tue emoticon preferite!
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Re: [gmx-users] Strange dgdl-value together with lincs

[Maik Goette]

Berk,

here comes the topology for this run (vdw morph):
Its OPLSAA and the hydrogens have bond terms. This is the standard 
OPLSAA FF for ethane and methanol.

Thanks.

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass 
typeBchargeB  massB
 1   opls_135  1E2M CB  10.0 12.011 
opls_1570.0 12.011
 2   opls_140  1E2MHB1  10.0  1.008 
opls_1560.0  1.008
 3   opls_140  1E2MHB2  10.0  1.008 
opls_1560.0  1.008
 4   opls_140  1E2MHB3  10.0  1.008 
opls_1560.0  1.008
 5   opls_135  1E2M CA  20.0 12.011 
opls_1540.015.9994
 6   opls_140  1E2MHA1  20.0  1.008 
opls_1550.0  1.008
 7   opls_140  1E2MHA2  20.0  1.008 
DUM0.0  1.008
 8   opls_140  1E2MHA3  20.0  1.008 
DUM0.0  1.008


[ bonds ]
;  aiaj functc0c1c2c3
1 2 1 0.10900284512.0 0.10900284512.0
1 3 1 0.10900284512.0 0.10900284512.0
1 4 1 0.10900284512.0 0.10900284512.0
1 5 1 0.15290224262.4 0.14100267776.0
5 6 1 0.10900284512.0 0.09450462750.4
5 7 1 0.10900284512.0 0.10900284512.0
5 8 1 0.10900284512.0 0.10900284512.0

[ pairs ]
;  aiaj functc0c1c2c3
2 6 1
2 7 1
2 8 1
3 6 1
3 7 1
3 8 1
4 6 1
4 7 1
4 8 1

[ angles ]
;  aiajak functc0c1c2 
 c3

2 1 3 1 107.800 276.144 107.800 276.144
2 1 4 1 107.800 276.144 107.800 276.144
2 1 5 1 110.700 313.800 109.500 292.880
3 1 4 1 107.800 276.144 107.800 276.144
3 1 5 1 110.700 313.800 109.500 292.880
4 1 5 1 110.700 313.800 109.500 292.880
1 5 6 1 110.700 313.800 108.500 460.240
1 5 7 1 110.700 313.800 110.700 313.800
1 5 8 1 110.700 313.800 110.700 313.800
6 5 7 1 107.800 276.144 107.800 276.144
6 5 8 1 107.800 276.144 107.800 276.144
7 5 8 1 107.800 276.144 107.800 276.144

[ dihedrals ]
;  aiajakal functc0c1c2 
   c3c4c5
2 1 5 6 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.94140 2.82420 0.0 
-3.76560 0.0 0.0
2 1 5 7 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.62760 1.88280 0.0 
-2.51040 0.0 0.0
2 1 5 8 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.62760 1.88280 0.0 
-2.51040 0.0 0.0
3 1 5 6 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.94140 2.82420 0.0 
-3.76560 0.0 0.0
3 1 5 7 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.62760 1.88280 0.0 
-2.51040 0.0 0.0
3 1 5 8 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.62760 1.88280 0.0 
-2.51040 0.0 0.0
4 1 5 6 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.94140 2.82420 0.0 
-3.76560 0.0 0.0
4 1 5 7 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.62760 1.88280 0.0 
-2.51040 0.0 0.0
4 1 5 8 3   0.62760 1.88280 0.0 
-2.51040 0.0 0.0 0.62760 1.88280 0.0 
-2.51040 0.0 0.0


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Berk Hess wrote:


I assume your are using a united atom model.
What are the bonded parameters for the methanol H
in the ethane topology?
Does it have the normal me

Re: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster

[OZGE ENGIN]

Thank you very much Mark, it is clear to me now! 

-Original Message-
From: [EMAIL PROTECTED]
To: Discussion list for GROMACS users 
Date: Fri, 15 Feb 2008 18:44:51 +1100
Subject: Re: Re: Re: [gmx-users] still got the problem with the output of 
g_cluster

So we're expecting a histogram of an all-against-all RMSD calculation over 
3000-odd elements. So we should expect that around 3000*3000*0.5 entries exist 
in the histogram... that's about 450 entries. That sounds familiar, now :-) 
For 3002 elements, excluding self-comparisons, there are 3001-choose-2 
combinations, i.e. 3001*3000*0.5, which is the number you give below. The 
values in this column are consistent with a histogram.

Mark

- Original Message -
From: OZGE ENGIN <[EMAIL PROTECTED]>
Date: Friday, February 15, 2008 6:32 pm
Subject: Re: Re: Re: [gmx-users] still got the problem with the output of 
g_cluster
To: gmx-users@gromacs.org
Cc: gmx-users@gromacs.org

> Sorry Mark, the sum of the 2 nd column is 4501500. The frame 
> number is 3002.
> 
> 
> -Original Message-
> From: [EMAIL PROTECTED]
> To: Discussion list for GROMACS users 
> Date: Fri, 15 Feb 2008 10:04:45 +1100
> Subject: Re: Re: [gmx-users] still got the problem with the 
> output of g_cluster
> 
> What's the sum of the second column?
> 
> Mark
> 
> - Original Message -
> From: OZGE ENGIN <[EMAIL PROTECTED]>
> Date: Friday, February 15, 2008 9:46 am
> Subject: Re: Re: [gmx-users] still got the problem with the 
> output of g_cluster
> To: gmx-users@gromacs.org
> 
> > Hi Mark,
> > 
> > You are right. While I am writing,most of the things in my 
> mind 
> > are lost :)
> > 
> > The actual command line is:
> > 
> > g_cluster -s .tpr -f .xtc -dist 
> > 
> > and it gives a output file named rmsd-dist.xvg. In the first 
> > column, the rmsd values are written. However, I can not 
> > understand the values in the second column, the title of 
> second 
> > column is only indicated. No explanation has been made in the 
> > manual. 
> > 
> > The frame number is 3000. One of the numbers on that column 
> > exceeds that value.
> > 
> > -Original Message-
> > From: Mark Abraham <[EMAIL PROTECTED]>
> > To: Discussion list for GROMACS users 
> > Date: Fri, 15 Feb 2008 09:11:55 +1100
> > Subject: Re: [gmx-users] still got the problem with the output 
> > of g_cluster
> > 
> > OZGE ENGIN wrote:
> > > Hi all,
> > > 
> > > I have still got the problem with the second column of the 
> > output of g_cluster with -dist option. Xavier said that the 
> a.u 
> > stands for arbitrary unit and I think it gives the histogram 
> of 
> > rmsd value distribution. If so, I can not understand why the 
> > total of this column is not equal to the total number of 
> > conformations obtained from the simulation.
> > 
> > Well, what is it equal to? How many frames are you using, what 
> > are your 
> > actual command lines? Can you provide a short excerpt of the 
> > .xvg file?
> > 
> > Please consider the point of view of the people of whom you're 
> > asking 
> > such a question. Unless they're actually fluent with the code 
> > and useage 
> > of g_cluster, they don't have the answer at their fingertips. 
> > However if 
> > you give them useful information, they might be able to see 
> > things that 
> > you can't. If you don't provide useful information, then even 
> > users who 
> > do have the answer at their fingertips might decide you're not 
> > worth 
> > their time :-)
> > 
> > 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
> > 
> > 
> > Ozge Engin
> > =
> > Computational Science & Engineering
> > Koc University
> > ___
> > 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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> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> Ozge Engin
> =
> Computational Science & Engineering
> Koc University
> _