date:20091009


Hi,

I ran your system and mdrun prints a VERY clear warning to stderr and to md.log:
WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the
forces deviate on average 164% from minus the numerical derivative of
the potential


I understand that Gromacs can be somewhat complicated for new users
and that things might go wrong when you try them the first time.
But you sent a large number of mails about your issues and several people have 
put time
into helping you out.
The least you could and should do is check your the output of your simulations.
This would have also cost you less time than actually sending questions to the 
mailing list.

I am fed up with spending time on helping a person find out what seemingly 
unexplainable crashes are,
when the output clearly tells you what the problem is.

I am very sorry to say so, but I will not help you any more on this topic.
Anyhow I think the problem should be solved now.

Berk

Date: Thu, 8 Oct 2009 15:58:41 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated 
potential - Problem

Hi Berk,
the potential I used comes indeed from Boltzmann inversion but I fitted it with 
a polynomial function of suitable degree which gave an almost perfect agreement 
on the range chosen (outside this range it reproduces the correct repulsive 
branches of the potential).  I generated the tabulated potential on the basis 
of this polynomial fitting and also the derivatives in the third coulmn of the 
table were calculated on the basis of the analytical derivative of the 
polynomial. Therefore, all the numerical noise has been removed. Maybe, are 
there numerical problems of any kind if the potential has a very large 
repulsive value on the repulsive branches? I any  case in my initial 
configuration all the bonds share value near the minimum and so they are not 
exploring these highly repulsive regions.
Thank you

AM



Messaggio originale

Da: g...@hotmail.com

Data: 8-ott-2009 9.12 AM

A: Discussion list for GROMACS usersgmx-users@gromacs.org

Ogg: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -
Problem






Hi,

The required spacing is basically only related with the second derivative of 
the potential
and the accuracy you want. In standard cases, your spacing of 0.001 nm should 
be enough.
But if your potential comes from some numerical inversion procedure, your 
potential could
be very noisy, which could result in nearly random forces, which could cause 
the system to crash.
Also the maximum time step you can take will depend on the second derivative of 
the potential.

Berk


Date: Thu, 8 Oct 2009 11:01:39 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -
Problem

Hi,

I used gmxcheck and gxmdump to compare the results of two simulations on an 
identical system but using two different tabulated potential, one harmonic (the 
simulation ended correctly) and one not. There are no differences in terms of 
non bonded interactions, other energy terms and the parameters of the 
simulation.
Therefore, it is still something related to the tabulated potential. Is there a 
minimum or a maximum number of (uniformly spaced) points suggested (or 
required) for a tabulated potential? In this case I used 1001 points to sample 
an interval from 0 to 1.0 nm. 
Many thanks,

AM



Messaggio originale
Da: mark.abra...@anu.edu.au
Data: 5-ott-2009 11.19 PM
A: Discussion list for GROMACS usersgmx-users@gromacs.org
Ogg: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem

albita...@virgilio.it wrote:
 Hi,
 I came back to my original stretching potential in tabulated form and I 
 have still problems...
 when running a geometry optimization the results are like that:
 
 **+
 ^MStep 635, Epot=2.259501e+02, Fnorm=4.086e+00, Fmax=1.886e+01 (atom 34)
 ^MStep 636, Epot=2.259499e+02, Fnorm=3.847e+00, Fmax=1.992e+01 (atom 33)
 ^MStep 637, Epot=2.259495e+02, Fnorm=1.002e+01, Fmax=5.408e+01 (atom 33)
 ^MStep 638, Epot=2.259449e+02, Fnorm=1.026e+01, Fmax=4.098e+01 (atom 34)
 ^MStep 639, Epot=2.259393e+02, Fnorm=2.193e+01, Fmax=1.159e+02 (atom 35)
 ^MStep 640, Epot=2.259364e+02, Fnorm=1.469e+01, Fmax=7.064e+01 (atom 34)
 ^MStep 641, Epot=2.259335e+02, Fnorm=1.281e+01, Fmax=7.154e+01 (atom 34)
 ^MStep 642, Epot=2.259315e+02, Fnorm=5.803e+00, Fmax=2.861e+01 (atom 35)
 ^MStep 643, Epot=2.259314e+02, Fnorm=6.332e+00, Fmax=3.116e+01 (atom 34)
 ^MStep 644, Epot=2.259310e+02, Fnorm=3.550e+00, Fmax=1.502e+01 (atom 34)
 
 Stepsize too small, or no change in energy.
 Converged to machine precision,
 but not to the requested precision Fmax  0.1
 
 
 as if the system is frozen. My system here is an isolated, linear and 
 finite-length chain.
 When

Re: [gmx-users] Free Energy




b95203...@ntu.edu.tw wrote:

Hi all,
I have some pdb file of peptides that I wish to do free energy calcuation.
Is there any source I can do that?


http://www.gromacs.org/Documentation/How-tos/Free_Energy_Calculations

If you want a more specific answer, ask a more specific question.

-Justin


Thanks
Regards,
William

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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R: RE: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem

2009-10-09 Thread albita...@virgilio.it

I asked your help since my tabulated potential reports in the third column the 
derivatives (minus the derivatives...to be precise) which are analitically 
exact with respect to the potential reported in the second column. So, in this 
case, these are the exact forces. If the numerical derivatives calculated by 
gromacs are so different now it is not a problem of my  input and no 
information are given to solve this problem...hence my request...
Furthermore, If derivatives are calculated by the code please explain me why I 
have to report them in the table? and where the code uses one or the others?
Probably, I am stupid or ignorant but since it's the first time I use a 
tabulated potential I could not find any precise answers to this questions.

I am not blind and I can read both my input/output files and also the 
manual...so I was aware of the WARNING. 
This does not change the fact that using the analytical derivatives (in 
numerical form) I have errors and for me this is nonsense.
obviously there should be an answer to this question but where is it? 
I don't think that my request was so stupid as you declare. If there are so 
many details which could affect the calculations please report and justify them 
explicitly in the documentation
anyway, thank you for your kind help.
I won't ask anything else about this problem and I will use my time lo learn 
reading.

AM





Messaggio originale

Da: g...@hotmail.com

Data: 9-ott-2009 9.58 AM

A: Discussion list for GROMACS usersgmx-users@gromacs.org

Ogg: RE: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated 
potential - Problem





--

Hi,

I ran your system and mdrun prints a VERY clear warning to stderr and to md.log:
WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the
forces deviate on average 164% from minus the numerical derivative of
the potential


I understand that Gromacs can be somewhat complicated for new users
and that things might go wrong when you try them the first time.
But you sent a large number of mails about your issues and several people have 
put time
into helping you out.
The least you could and should do is check your the output of your simulations.
This would have also cost you less time than actually sending questions to the 
mailing list.

I am fed up with spending time on helping a person find out what seemingly 
unexplainable crashes are,
when the output clearly tells you what the problem is.

I am very sorry to say so, but I will not help you any more on this topic.
Anyhow I think the problem should be solved now.

Berk

Date: Thu, 8 Oct 2009 15:58:41 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated 
potential - Problem

Hi Berk,
the potential I used comes indeed from Boltzmann inversion but I fitted it with 
a polynomial function of suitable degree which gave an almost perfect agreement 
on the range chosen (outside this range it reproduces the correct repulsive 
branches of the potential).  I generated the tabulated potential on the basis 
of this polynomial fitting and also the derivatives in the third coulmn of the 
table were calculated on the basis of the analytical derivative of the 
polynomial. Therefore, all the numerical noise has been removed. Maybe, are 
there numerical problems of any kind if the potential has a very large 
repulsive value on the repulsive branches? I any  case in my initial 
configuration all the bonds share value near the minimum and so they are not 
exploring these highly repulsive regions.
Thank you

AM



Messaggio originale

Da: g...@hotmail.com

Data: 8-ott-2009 9.12 AM

A: Discussion list for GROMACS usersgmx-users@gromacs.org

Ogg: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -
Problem






Hi,

The required spacing is basically only related with the second derivative of 
the potential
and the accuracy you want. In standard cases, your spacing of 0.001 nm should 
be enough.
But if your potential comes from some numerical inversion procedure, your 
potential could
be very noisy, which could result in nearly random forces, which could cause 
the system to crash.
Also the maximum time step you can take will depend on the second derivative of 
the potential.

Berk


Date: Thu, 8 Oct 2009 11:01:39 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -
Problem

Hi,

I used gmxcheck and gxmdump to compare the results of two simulations on an 
identical system but using two different tabulated potential, one harmonic (the 
simulation ended correctly) and one not. There are no differences in terms of 
non bonded interactions, other energy terms and the parameters of the 
simulation.
Therefore, it is still something related to the tabulated potential. Is there a 
minimum or a maximum number of (uniformly spaced) points suggested (or 
required)

RE: R: RE: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem


OK, I'll answer once more.



You are apparently convinced you are doing the right thing.

But if you have a problem and want someone to help you,

you should report all warnings you get so users do not waste their time

(and your time) helping you. Mentioning this warning right away

would have saved you and us a lot of work.



I had a look at your table and I would guess you force is simply

a factor 10 too large (you might have scaled from Angstroms to nm

or something like that and forgot to scale the force).

The code only determines an approximation of the derivative to

be able to give the warning it gave you.



Berk


Date: Fri, 9 Oct 2009 13:17:45 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated  
potential - Problem

I asked your help since my tabulated potential reports in the third column the 
derivatives (minus the derivatives...to be precise) which are analitically 
exact with respect to the potential reported in the second column. So, in this 
case, these are the exact forces. If the numerical derivatives calculated by 
gromacs are so different now it is not a problem of my  input and no 
information are given to solve this problem...hence my request...
Furthermore, If derivatives are calculated by the code please explain me why I 
have to report them in the table? and where the code uses one or the others?
Probably, I am stupid or ignorant but since it's the first time I use a 
tabulated potential I could not find any precise answers to this questions.

I am not blind and I can read both my input/output files and also the 
manual...so I was aware of the WARNING. 
This does not change the fact that using the analytical derivatives (in 
numerical form) I have errors and for me this is nonsense.
obviously there should be an answer to this question but where is it? 
I don't think that my request was so stupid as you declare. If there are so 
many details which could affect the calculations please report and justify them 
explicitly in the documentation
anyway, thank you for your kind help.
I won't ask anything else about this problem and I will use my time lo learn 
reading.

AM





Messaggio originale

Da: g...@hotmail.com

Data: 9-ott-2009 9.58 AM

A: Discussion list for GROMACS usersgmx-users@gromacs.org

Ogg: RE: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated 
potential - Problem






Hi,

I ran your system and mdrun prints a VERY clear warning to stderr and to md.log:
WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the
forces deviate on average 164% from minus the numerical derivative of
the potential


I understand that Gromacs can be somewhat complicated for new users
and that things might go wrong when you try them the first time.
But you sent a large number of mails about your issues and several people have 
put time
into helping you out.
The least you could and should do is check your the output of your simulations.
This would have also cost you less time than actually sending questions to the 
mailing list.

I am fed up with spending time on helping a person find out what seemingly 
unexplainable crashes are,
when the output clearly tells you what the problem is.

I am very sorry to say so, but I will not help you any more on this topic.
Anyhow I think the problem should be solved now.

Berk

Date: Thu, 8 Oct 2009 15:58:41 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated 
potential - Problem

Hi Berk,
the potential I used comes indeed from Boltzmann inversion but I fitted it with 
a polynomial function of suitable degree which gave an almost perfect agreement 
on the range chosen (outside this range it reproduces the correct repulsive 
branches of the potential).  I generated the tabulated potential on the basis 
of this polynomial fitting and also the derivatives in the third coulmn of the 
table were calculated on the basis of the analytical derivative of the 
polynomial. Therefore, all the numerical noise has been removed. Maybe, are 
there numerical problems of any kind if the potential has a very large 
repulsive value on the repulsive branches? I any  case in my initial 
configuration all the bonds share value near the minimum and so they are not 
exploring these highly repulsive regions.
Thank you

AM



Messaggio originale

Da: g...@hotmail.com

Data: 8-ott-2009 9.12 AM

A: Discussion list for GROMACS usersgmx-users@gromacs.org

Ogg: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -
Problem






Hi,

The required spacing is basically only related with the second derivative of 
the potential
and the accuracy you want. In standard cases, your spacing of 0.001 nm should 
be enough.
But if your potential comes from some numerical inversion procedure, your 
potential could
be very noisy, which could result in

[gmx-users] Tips and tricks to make your own coarse-grained model?

2009-10-09 Thread ms

Hi,

First of all, I am new to Gromacs and quite new to the MD field (I had a
read of the Daan-Frenkel book and played very little with custom CG
models - I used to be an experimental guy), so please bear with me if
questions happen to be naive.

My aim is to re-implement a formerly standalone CG model by mean of gmx.
It seems that gmx is well suited to the task; however I understand that
there is an incredible number of pitfalls where a newbie fall in.

I am currently reading and re-reading the manual, looking at the online
docs and tutorials. But most of information, understandably, refer to
all-atom modeling and there is little on how to build your own model on gmx.

Maybe my googling skills are not as good as once they were -in this case
can anyone point me to any page where this kind of task is documented?

If such a page there isn't (and even if there is), I would appreciate a
lot if anyone of you can share your wisdom on best practices, pitfalls,
things to know etc. before diving head-on in such an endeavour.

Thanks a lot!

Massimo
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Re: [gmx-users] Tips and tricks to make your own coarse-grained model?

2009-10-09 Thread ms

Justin A. Lemkul ha scritto:
 My aim is to re-implement a formerly standalone CG model by mean of gmx.
 It seems that gmx is well suited to the task; however I understand that
 there is an incredible number of pitfalls where a newbie fall in.

 I am currently reading and re-reading the manual, looking at the online
 docs and tutorials. But most of information, understandably, refer to
 all-atom modeling and there is little on how to build your own model
 on gmx.

 Maybe my googling skills are not as good as once they were -in this case
 can anyone point me to any page where this kind of task is documented?

 If such a page there isn't (and even if there is), I would appreciate a
 lot if anyone of you can share your wisdom on best practices, pitfalls,
 things to know etc. before diving head-on in such an endeavour.

 
 So, to clarify, this is an already-existing CG model that you simply
 want to use for simulations in Gromacs?  It is then rather easy.  You
 need to define all appropriate force field files (nb.itp, bon.itp, .atp,
 etc), and perhaps .rtp files if you can also come up with a way to
 define an appropriate CG input for pdb2gmx.

Yes. I know the specs of the cg model, and I want to re-implement it
within gromacs. Actually it is a class of related models. I'd start from
a very minimal one and then improve gradually.

I understand I have to define all appropriate FF files, but I wonder
what is the best way to do it, what documentation to learn by heart,
what sanity checks... You make me optimist in saying it is rather easy
, but science is always full of traps, especially for the newcomer...

thanks!
m.
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Re: [gmx-users] Tips and tricks to make your own coarse-grained model?




ms wrote:

Justin A. Lemkul ha scritto:

My aim is to re-implement a formerly standalone CG model by mean of gmx.
It seems that gmx is well suited to the task; however I understand that
there is an incredible number of pitfalls where a newbie fall in.

I am currently reading and re-reading the manual, looking at the online
docs and tutorials. But most of information, understandably, refer to
all-atom modeling and there is little on how to build your own model
on gmx.

Maybe my googling skills are not as good as once they were -in this case
can anyone point me to any page where this kind of task is documented?

If such a page there isn't (and even if there is), I would appreciate a
lot if anyone of you can share your wisdom on best practices, pitfalls,
things to know etc. before diving head-on in such an endeavour.


So, to clarify, this is an already-existing CG model that you simply
want to use for simulations in Gromacs?  It is then rather easy.  You
need to define all appropriate force field files (nb.itp, bon.itp, .atp,
etc), and perhaps .rtp files if you can also come up with a way to
define an appropriate CG input for pdb2gmx.


Yes. I know the specs of the cg model, and I want to re-implement it
within gromacs. Actually it is a class of related models. I'd start from
a very minimal one and then improve gradually.

I understand I have to define all appropriate FF files, but I wonder
what is the best way to do it, what documentation to learn by heart,
what sanity checks... You make me optimist in saying it is rather easy
, but science is always full of traps, especially for the newcomer...



If the model has been created, tested, and validated, the hardest work is done. 
 You just have to type in a text editor to put it all together :)  If you are 
looking to derive new parameters, well, then that certainly is quite difficult:


http://www.gromacs.org/Documentation/How-tos/Parametrization

Chapter 5 in the manual contains all the information necessary (in terms of both 
syntax and content) for producing the necessary files.  It should be the first 
port of call when questions arise.


-Justin


thanks!
m.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] user defined potential function for 1-4 interaction

2009-10-09 Thread M Hafizur Rahman

I think there must be a way in gromacs to pass tabulated potenttial for 1-4 
interaction for two groups as interaction between different pairs can be 
significantly different and can change the structure of an indiviual molecule. 
I would request:  Please let me know if it is possible to pass tabulated 
potential for pair inteaction for two groups. if my method, which you will see 
below, is wrong please let me know the correct way. I searched previous 
communications regarding tabulated potential but could not get my answer. I 
hope I am not wasing your time.

Thanks.


- Original Message - 
  From: LuLanyuan 
  To: gmx-users@gromacs.org 
  Sent: Thursday, October 08, 2009 8:04 PM
  Subject: RE: [gmx-users] user defined potential function for 1-4 interaction


  Hi,
  As I remember, you can only use one table for 1-4 interactions. Don't know if 
it's changed
  in the latest version.
  Lanyuan

   From: mhrah...@dal.ca
   To: gmx-users@gromacs.org
   Subject: Re: [gmx-users] user defined potential function for 1-4 interaction
   Date: Thu, 8 Oct 2009 19:10:39 -0300
   
   Hi all:
   I posted this earlier but did not get any help I really need to slove this 
   issue.
   
   What should be the way to pass a formatted table for the 1-4 interaction
   for two or more different groups? Reading page 150 and 180 of manual 4.0, 
   I
   understand user defined potential functions can be passed for many groups
   using energygrp_table in .mdp file but nothing is clearly mentioned
   regarding pair interaction
   
   I have two grps for 1-4 interactions MTN and SFT.
   mdrun command includes:
   -table table.xvg -tablep pair.xvg
   ; .mdp file contains,
   energygrps = MTN SFT
   energygrp_table: MTN MTN MTN SFT
   
   I passed three tables for pair interaction in the
   name pair.xvg, pair_MTN_MTN.xvg and pair_MTN_SFT.xvg.
   I see the later two tabels are not recognized. If pair_MTN_MTN.xvg and 
   pair_MTN_SFT.xvg are not supplied GROMACS donot issue any warning.
   I am afraid that I failed to submit separate table for pair interaction 
   properly in this way.
   
   Thanks,
   M.H.Rahman 
   
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--


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[gmx-users] g_mindist

2009-10-09 Thread Christian Seifert

Dear Mr. Gromacs, ;-)
and hello to everybody!

When I use g_mindist with a Syntax like this:
g_mindist -f ./prot.xtc -s ./prot.tpr -n ./prot.ndx
-od ./protein_self.xvg -o prot.out -pi

Then I just get the xvg file with the distance of the group (I selected
C-alphas) with its periodic image. The xvg file look familiar and
correct, but the prot.out file is not created. There is no warning or
error.

I used g_mindist v4.0.5.

Greetings,
Christian

-- 
M.Sc. Christian Seifert
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: cseif...@bph.rub.de
Web: http://www.bph.rub.de

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RE: [gmx-users] user defined potential function for 1-4 interaction


Hi,

Unfortunately this is not possible.
If you do not have to many pairs, you can change all (or all minus one type)
from pairs to tabulated bonds (bonds type 9) in your topology.
Then you can supply as many different bond tables as you like.
Note that this will supply a single potential though,
not separate Coulomb, dispersion and repulsion tables.

Berk

From: mhrah...@dal.ca
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] user defined potential function for 1-4 interaction
Date: Fri, 9 Oct 2009 09:48:19 -0300










I think there must be a way in gromacs to pass tabulated 
potenttial for 1-4 interaction for two groups as interaction between 
different pairs can be significantly different and can change the structure of 
an indiviual molecule. 
I would request:  Please let me know if it is 
possible to pass tabulated potential for pair inteaction for two groups. if 
my method, which you will see below, is wrong please let me know the 
correct way. I searched previous communications regarding tabulated potential 
but could not get my answer. I hope I am not wasing your time.
 
Thanks.
 
 
- Original Message - 

  From: 
  LuLanyuan 

  To: gmx-users@gromacs.org 
  Sent: Thursday, October 08, 2009 8:04 
  PM
  Subject: RE: [gmx-users] user defined 
  potential function for 1-4 interaction
  
Hi,
As I remember, you can only use one table for 1-4 
  interactions. Don't know if it's changed
in the latest 
  version.
Lanyuan

 From: mhrah...@dal.ca
 To: gmx-users@gromacs.org
 Subject: 
  Re: [gmx-users] user defined potential function for 1-4 interaction
 
  Date: Thu, 8 Oct 2009 19:10:39 -0300
 
 Hi all:
 I posted 
  this earlier but did not get any help I really need to slove this 
 
  issue.
 
 What should be the way to pass a formatted table for 
  the 1-4 interaction
 for two or more different groups? Reading page 150 
  and 180 of manual 4.0, 
 I
 understand user defined potential 
  functions can be passed for many groups
 using energygrp_table in .mdp 
  file but nothing is clearly mentioned
 regarding pair 
  interaction
 
 I have two grps for 1-4 interactions MTN and 
  SFT.
 mdrun command includes:
 -table table.xvg -tablep 
  pair.xvg
 ; .mdp file contains,
 energygrps = MTN SFT
 
  energygrp_table: MTN MTN MTN SFT
 
 I passed three tables for 
  pair interaction in the
 name pair.xvg, pair_MTN_MTN.xvg and 
  pair_MTN_SFT.xvg.
 I see the later two tabels are not recognized. If 
  pair_MTN_MTN.xvg and 
 pair_MTN_SFT.xvg are not supplied GROMACS donot 
  issue any warning.
 I am afraid that I failed to submit separate table 
  for pair interaction 
 properly in this way.
 
 
  Thanks,
 M.H.Rahman 
 
 
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[gmx-users] Hard sphere simulation

2009-10-09 Thread osmair oliveira


Hi,
I would like to simulate hard sphere with different  
charge values (e.g. +30),  with different diameters (e.g. 5 nm)
 and with different values of Lennard-Jones. 
In addiction, in these models of the hard sphere
I would like to insert dipole (e.g. 15 Debye). 
So, is this possible to simulate these models in GROMACS?

Thanks,
Pos-doc. Osmair V. Oliveira
Federal University of Sao Carlos -  Brazil  
  
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RE: [gmx-users] g_mindist

Hi,

If you use -pi with g_mindist, all the other output options are ignored.

Berk

 Date: Fri, 9 Oct 2009 14:24:00 +0200
 From: cseif...@bph.ruhr-uni-bochum.de
 To: gmx-users@gromacs.org
 Subject: [gmx-users] g_mindist

 Dear Mr. Gromacs, ;-)
 and hello to everybody!

 When I use g_mindist with a Syntax like this:
 g_mindist -f ./prot.xtc -s ./prot.tpr -n ./prot.ndx
 -od ./protein_self.xvg -o prot.out -pi

 Then I just get the xvg file with the distance of the group (I selected
 C-alphas) with its periodic image. The xvg file look familiar and
 correct, but the prot.out file is not created. There is no warning or
 error.

 I used g_mindist v4.0.5.

 Greetings,
 Christian

 -- 
 M.Sc. Christian Seifert
 Department of Biophysics
 University of Bochum
 ND 04/67
 44780 Bochum
 Germany
 Tel: +49 (0)234 32 28363
 Fax: +49 (0)234 32 14626
 E-Mail: cseif...@bph.rub.de
 Web: http://www.bph.rub.de

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Re: [gmx-users] LINCS error




Yongchul Chung wrote:

Hi again gmx-users,

I ran into LINCS error again when I tried to incorporate pressure 
scaling parameters.
It seems like the initial pressure and temperature is erroneously large 
as shown in the md.log file below. can anyone tell me how to fix this?




Did you run energy minimization first?

-Justin


Thanks

Input Parameters:
   integrator   = md
   nsteps   = 10
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 10
   nstxout  = 500
   nstvout  = 1000
   nstfout  = 0
   nstenergy= 10
   nstxtcout= 0
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 0
   nky  = 0
   nkz  = 0
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = TRUE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = V-rescale
   epc  = Berendsen
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 1.01325e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  1.01325e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  1.01325e+00}
   compress (3x3):
  compress[0]={ 4.5e-03,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  4.5e-03,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  4.5e-03}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 1
   rtpi = 0.05
   coulombtype  = Cut-off
   rcoulomb_switch  = 0
   rcoulomb = 1.4
   vdwtype  = Cut-off
   rvdw_switch  = 0
   rvdw = 1.4
   epsilon_r= 1
   epsilon_rf   = 1
   tabext   = 1
   implicit_solvent = No
   gb_algorithm = Still
   gb_epsilon_solvent   = 80
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   gb_obc_alpha = 1
   gb_obc_beta  = 0.8
   gb_obc_gamma = 4.85
   sa_surface_tension   = 2.092
   DispCorr = No
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 0
   sc_sigma = 0.3
   delta_lambda = 0
   nwall= 0
   wall_type= 9-3
   wall_atomtype[0] = -1
   wall_atomtype[1] = -1
   wall_density[0]  = 0
   wall_density[1]  = 0
   wall_ewald_zfac  = 3
   pull = no
   disre= No
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc= 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc= 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   em_stepsize  = 0.01
   em_tol   = 10
   niter= 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr= 10
   ConstAlg = Lincs
   shake_tol= 0.0001
   lincs_order  = 4
   lincs_warnangle  = 30
   lincs_iter   = 1
   bd_fric  = 0
   ld_seed  = 1993
   cos_accel= 0
   deform (3x3):
  deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   userint1 = 0
   userint2 = 0
   userint3 = 0
   userint4 = 0
   userreal1= 0
   userreal2= 0
   userreal3= 0
   userreal4= 0
grpopts:
   nrdf:   11297
   ref_t: 300
   tau_t: 0.1
anneal:  No
ann_npoints:   0
   acc:   0   0   0
   nfreeze:   N   N   N
   energygrp_flags[  0]: 0
   efield-x:
  n = 0
   efield-xt:
  n = 0
   efield-y:
  n = 0
   efield-yt:
  n = 0
   efield-z:
  n = 0
   efield-zt:
  n = 0
   bQMMM= FALSE
   QMconstraints= 0
   QMMMscheme   = 0
   scalefactor  = 1
qm_opts:
   ngQM = 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 1   Coulomb: 1.4   LJ: 1.4
System total charge: -0.000
Configuring

Re: [gmx-users] LINCS error




Yongchul Chung wrote:

yes I carried out energy minimization and used following parameters.



OK, so what values of potential energy and maximum force did EM achieve?

-Justin


title   =  FWS
cpp =  /usr/bin/cpp ; the c pre-processor 
define  =  -DFLEXIBLE

constraints =  none
integrator  =  steep
dt  =  0.002; ps !
nsteps  =  1000
nstlist =  10 
ns_type =  grid

rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdwtype =  cut-off
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order  =  4
ewald_rtol  =  1e-5
optimize_fft  =  yes
;
;   Energy minimizing stuff
;
emtol   =  500
emstep  =  0.01




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] LINCS error

2009-10-09 Thread Yongchul Chung

After EM, I got:

Potential Energy  =  1.7242092e+05
Maximum force =  2.1079963e+03 on atom 675
Norm of force =  5.9417034e+01

I think my system size is too big compared to the box size so I am going to
run the simulation with smaller number of molecules to see whether this
helps or not.


On Fri, Oct 9, 2009 at 11:22 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Yongchul Chung wrote:

 yes I carried out energy minimization and used following parameters.


 OK, so what values of potential energy and maximum force did EM achieve?

 -Justin

  title   =  FWS
 cpp =  /usr/bin/cpp ; the c pre-processor define
=  -DFLEXIBLE
 constraints =  none
 integrator  =  steep
 dt  =  0.002; ps !
 nsteps  =  1000
 nstlist =  10 ns_type =  grid
 rlist   =  1.0
 coulombtype =  PME
 rcoulomb=  1.0
 vdwtype =  cut-off
 rvdw=  1.4
 fourierspacing  =  0.12
 fourier_nx  =  0
 fourier_ny  =  0
 fourier_nz  =  0
 pme_order  =  4
 ewald_rtol  =  1e-5
 optimize_fft  =  yes
 ;
 ;   Energy minimizing stuff
 ;
 emtol   =  500
 emstep  =  0.01



 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 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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-- 
Yongchul Greg Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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Re: [gmx-users] LINCS error




Yongchul Chung wrote:

After EM, I got:

Potential Energy  =  1.7242092e+05
Maximum force =  2.1079963e+03 on atom 675
Norm of force =  5.9417034e+01

I think my system size is too big compared to the box size so I am going 
to run the simulation with smaller number of molecules to see whether 
this helps or not.




Well, it could be that things are too jam-packed.  Note that you have an 
extremely repulsive potential energy, and a very large Fmax.  Using the atom 
number printed, you should be able to deduce the location of this large force, 
and hopefully the source, which is likely causing your explosion.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

2009-10-09 Thread João M . Damas

What do you mean by mutually inconsistent? From what I understand, they
aren't.

Also, [bonds] type 6 won't work for what I want, since I don't want to keep
the molecules at a fixed distance but to prevent them from coming closer,
i.e. I want a potential that depends on the distance between the atoms.

Testing the distance restraints can be quite exhaustive when you have about
160 restraints, and I am considering just the test case I'm trying, not the
actual system which will have some more organic molecules, which will lead
to a greater amount of combination of restraints...

Thanks,
João

On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

 João M. Damas wrote:

 Gromacs users,

 I have a small test system of about 2500 atoms which consists on a few
 organic molecules in a box of water. I'm trying to use distance restraints
 to keep each molecule apart from each other and I've failed until now.

 I'll start by saying that the simulation runs smoothly without using
 distance restraints and that I've created a single molecule topology that
 describes all organic molecules, allowing the use of distance restraints. By
 applying just one distance restraint between two atoms of different
 molecules, the simulation still runs without problems. When I apply all the
 distance restraints I want, the system crashes in the first few steps with
 an XTC error, which is preceded by a few inconsistent shifts and some LINCS
 warnings. Varying the number of restraints that I use, makes the crash
 happen at later steps (500ish), meanwhile giving a lot of inconsistent
 shifts before crashing with a fatal error: Number of grid cells is zero. I
 know it seems I'm experimenting blindly, but varying the number of
 restraints was the first that occurred to me.
 I've searched the list for similar problems and tried a few more tests.
 I've turned off LINCS and reduced the time step and it didn't solve the
 problem, the box blew up after a few steps due to pressure problems. Since
 it could be a PBC problem, I tried to increase the size of the box, but it
 didn't solve the problem. Turning of PBC did solve the problem, but I really
 need PBC. I've also changed the low, up1 and up2 to values inferior to half
 the box size (I don't even care about the up1 and up2 values in this
 application, and I was setting them to 5.0 nm before), but it didn't solve
 the problem either. I'm a little on a dead end here and I was hoping anyone
 could give me some insight.

 By the way, I'm using GROMACS 4.


 The simplest explanation is that your sets of distance restraints are
 mutually inconsistent. This destabilizes the system and eventually leads to
 your symptoms. Consider using [bonds] type 6, per advice of manual section
 4.3.4. Either way, if you add these restraints one by one after testing that
 the previous set seemed to work OK (didn't crash, trajectory looks right),
 you may uncover your issue.

 Mark
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

2009-10-09 Thread Mark Abraham


João M. Damas wrote:
What do you mean by mutually inconsistent? From what I understand, they 
aren't.


I mean a set for which there is no molecular arrangement that satisfies.

Also, [bonds] type 6 won't work for what I want, since I don't want to 
keep the molecules at a fixed distance but to prevent them from coming 
closer, i.e. I want a potential that depends on the distance between the 
atoms.


Testing the distance restraints can be quite exhaustive when you have 
about 160 restraints, and I am considering just the test case I'm 
trying, not the actual system which will have some more organic 
molecules, which will lead to a greater amount of combination of 
restraints...


#ifdef is your friend here...

[ distance_restraints ]

set to test now 

#ifdef BLAHBLAH

set to test later

#endif

Now you just move the #ifdef to rearrange your test cases.

I might start with an even smaller test case until you prove you can 
deal with both the input formatting issues and the physics issues with 
it. Testing will be faster, for starters.


Mark

On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham mark.abra...@anu.edu.au 
mailto:mark.abra...@anu.edu.au wrote:


João M. Damas wrote:

Gromacs users,

I have a small test system of about 2500 atoms which consists on
a few organic molecules in a box of water. I'm trying to use
distance restraints to keep each molecule apart from each other
and I've failed until now.

I'll start by saying that the simulation runs smoothly without
using distance restraints and that I've created a single
molecule topology that describes all organic molecules, allowing
the use of distance restraints. By applying just one distance
restraint between two atoms of different molecules, the
simulation still runs without problems. When I apply all the
distance restraints I want, the system crashes in the first few
steps with an XTC error, which is preceded by a few inconsistent
shifts and some LINCS warnings. Varying the number of restraints
that I use, makes the crash happen at later steps (500ish),
meanwhile giving a lot of inconsistent shifts before crashing
with a fatal error: Number of grid cells is zero. I know it
seems I'm experimenting blindly, but varying the number of
restraints was the first that occurred to me.
I've searched the list for similar problems and tried a few more
tests. I've turned off LINCS and reduced the time step and it
didn't solve the problem, the box blew up after a few steps due
to pressure problems. Since it could be a PBC problem, I tried
to increase the size of the box, but it didn't solve the
problem. Turning of PBC did solve the problem, but I really need
PBC. I've also changed the low, up1 and up2 to values inferior
to half the box size (I don't even care about the up1 and up2
values in this application, and I was setting them to 5.0 nm
before), but it didn't solve the problem either. I'm a little on
a dead end here and I was hoping anyone could give me some insight.

By the way, I'm using GROMACS 4.


The simplest explanation is that your sets of distance restraints
are mutually inconsistent. This destabilizes the system and
eventually leads to your symptoms. Consider using [bonds] type 6,
per advice of manual section 4.3.4. Either way, if you add these
restraints one by one after testing that the previous set seemed to
work OK (didn't crash, trajectory looks right), you may uncover your
issue.

Mark
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613




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[gmx-users] creating a larger lipid membrane

Dear Gromacs Users,
I have been trying to generate a larger lipid system but am running into
troubles due to improper initial co-ordinates set up. Following are the
steps i am trying to follow.

1. I start with a 128 dppc membrane and use genconf to create a larger
system. I got the dppc128.pdb from Dr. Peter Tieleman's website.

2. I changed my topology file accordingly (change the number of DPPC and
Water molecules)

3. I move on to energy minimization. During the mdrun i see the following
message :-

Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is
larger than the 1-4 table size 2.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

I also notice that the max force does not converge to less than 2000 rather
its of the order of 2e+06 .

4. I tried to do energy minimization again on the above system but the
steepest descent could not change the potential energy substantially and
terminated after less that 20 steps. I again noticed the following warning

Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is
larger than the 1-4 table size 2.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc =
xyz has been used as default.

Same warnings were printed out during energy minimization.

6. I also tried to use the table-extension option and increased its value to
10 nm but later the LINCS printed out too many warnings and MD could not be
done. I know that its not at all a good idea to increase the 1-4 cut off.

By the way to be specific the system size was 12 x 12 x 6 in nm3. I had 256
lipids and about 7300 water molecules.


I believe that this might not be the best way to create a larger bilayer
system. Could somebody suggest me other ways of doing this?

Any help will be appreciated thank you

Amit
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Re: [gmx-users] creating a larger lipid membrane




Amit Choubey wrote:

Dear Gromacs Users,

I have been trying to generate a larger lipid system but am running into 
troubles due to improper initial co-ordinates set up. Following are the 
steps i am trying to follow.


1. I start with a 128 dppc membrane and use genconf to create a larger 
system. I got the dppc128.pdb from Dr. Peter Tieleman's website.




Did you correct for periodicity before you extended the system?  The files 
distributed by Tieleman are compact representations.


2. I changed my topology file accordingly (change the number of DPPC and 
Water molecules)


3. I move on to energy minimization. During the mdrun i see the 
following message :-


Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which 
is larger than the 1-4 table size 2.800 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size



Looks to me like two bonded atoms are across the box from each other, which 
seems to answer my question above :)


I also notice that the max force does not converge to less than 2000 
rather its of the order of 2e+06 .


4. I tried to do energy minimization again on the above system but the 
steepest descent could not change the potential energy substantially and 
terminated after less that 20 steps. I again noticed the following warning 

Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which 
is larger than the 1-4 table size 2.800 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc 
= xyz has been used as default.




Bad idea.  This option is for infinite molecules, like nanotubes or graphene 
sheets that are supposed to extend across the simulation box.



Same warnings were printed out during energy minimization.

6. I also tried to use the table-extension option and increased its 
value to 10 nm but later the LINCS printed out too many warnings and MD 
could not be done. I know that its not at all a good idea to increase 
the 1-4 cut off.




The standard advice is to fix the problem with the system, not change the 
table-extension.


By the way to be specific the system size was 12 x 12 x 6 in nm3. I had 
256 lipids and about 7300 water molecules.
 

I believe that this might not be the best way to create a larger bilayer 
system. Could somebody suggest me other ways of doing this?




Fix periodicity, then use genconf.

-Justin


Any help will be appreciated thank you

Amit





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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] creating a larger lipid membrane

2009-10-09 Thread Mark Abraham


Amit Choubey wrote:

Dear Gromacs Users,

I have been trying to generate a larger lipid system but am running into 
troubles due to improper initial co-ordinates set up. Following are the 
steps i am trying to follow.


1. I start with a 128 dppc membrane and use genconf to create a larger 
system. I got the dppc128.pdb from Dr. Peter Tieleman's website.


What command line did you use?

2. I changed my topology file accordingly (change the number of DPPC and 
Water molecules)


3. I move on to energy minimization. During the mdrun i see the 
following message :-


Test your protocol on the original coordinate file. It needs to work for 
 your procedure to be sound.


Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which 
is larger than the 1-4 table size 2.800 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

I also notice that the max force does not converge to less than 2000 
rather its of the order of 2e+06 .


4. I tried to do energy minimization again on the above system but the 
steepest descent could not change the potential energy substantially and 
terminated after less that 20 steps. I again noticed the following warning 

Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which 
is larger than the 1-4 table size 2.800 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc 
= xyz has been used as default.


Same warnings were printed out during energy minimization.


You don't have periodic molecules. Changing mdp options haphazardly is a 
recipe for problems. Read 7.3 about them in the first instance, and then 
look up in the table of contents for more background.


6. I also tried to use the table-extension option and increased its 
value to 10 nm but later the LINCS printed out too many warnings and MD 
could not be done. I know that its not at all a good idea to increase 
the 1-4 cut off.


Yup, bad idea. Fix the underlying problem, not the symptoms.

Mark
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Re: [gmx-users] creating a larger lipid membrane

Hi Justin,
Yes you are right. I didnt fix the periodicity to start with. Could you tell
me how to do that, which command to work with?
Thanks.

amit

On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Dear Gromacs Users,

 I have been trying to generate a larger lipid system but am running into
 troubles due to improper initial co-ordinates set up. Following are the
 steps i am trying to follow.

 1. I start with a 128 dppc membrane and use genconf to create a larger
 system. I got the dppc128.pdb from Dr. Peter Tieleman's website.


 Did you correct for periodicity before you extended the system?  The files
 distributed by Tieleman are compact representations.

  2. I changed my topology file accordingly (change the number of DPPC and
 Water molecules)

 3. I move on to energy minimization. During the mdrun i see the following
 message :-

 Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is
 larger than the 1-4 table size 2.800 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size


 Looks to me like two bonded atoms are across the box from each other, which
 seems to answer my question above :)

  I also notice that the max force does not converge to less than 2000
 rather its of the order of 2e+06 .

 4. I tried to do energy minimization again on the above system but the
 steepest descent could not change the potential energy substantially and
 terminated after less that 20 steps. I again noticed the following warning
 Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is
 larger than the 1-4 table size 2.800 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc =
 xyz has been used as default.


 Bad idea.  This option is for infinite molecules, like nanotubes or
 graphene sheets that are supposed to extend across the simulation box.

  Same warnings were printed out during energy minimization.

 6. I also tried to use the table-extension option and increased its value
 to 10 nm but later the LINCS printed out too many warnings and MD could not
 be done. I know that its not at all a good idea to increase the 1-4 cut off.


 The standard advice is to fix the problem with the system, not change the
 table-extension.

  By the way to be specific the system size was 12 x 12 x 6 in nm3. I had
 256 lipids and about 7300 water molecules.

 I believe that this might not be the best way to create a larger bilayer
 system. Could somebody suggest me other ways of doing this?


 Fix periodicity, then use genconf.

 -Justin

  Any help will be appreciated thank you

 Amit



 

 ___
 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!
 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/mailing_lists/users.php


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 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/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/mailing_lists/users.php

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Re: [gmx-users] creating a larger lipid membrane

Hi Mark,
Yes i checked the procedure on the original structure. It woks fine. As for
genconf i used the following

genconf -f dppc128.pdb -o out.gro -nbox 2 2 1

As Justin pointed out, I did not correct the periodicity of original
structure before using genconf .

Thank you,
Amit

On Fri, Oct 9, 2009 at 5:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 Amit Choubey wrote:

 Dear Gromacs Users,

 I have been trying to generate a larger lipid system but am running into
 troubles due to improper initial co-ordinates set up. Following are the
 steps i am trying to follow.

 1. I start with a 128 dppc membrane and use genconf to create a larger
 system. I got the dppc128.pdb from Dr. Peter Tieleman's website.


 What command line did you use?

  2. I changed my topology file accordingly (change the number of DPPC and
 Water molecules)

 3. I move on to energy minimization. During the mdrun i see the following
 message :-


 Test your protocol on the original coordinate file. It needs to work for
  your procedure to be sound.

  Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is
 larger than the 1-4 table size 2.800 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 I also notice that the max force does not converge to less than 2000
 rather its of the order of 2e+06 .

 4. I tried to do energy minimization again on the above system but the
 steepest descent could not change the potential energy substantially and
 terminated after less that 20 steps. I again noticed the following warning
 Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is
 larger than the 1-4 table size 2.800 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc =
 xyz has been used as default.

 Same warnings were printed out during energy minimization.


 You don't have periodic molecules. Changing mdp options haphazardly is a
 recipe for problems. Read 7.3 about them in the first instance, and then
 look up in the table of contents for more background.

  6. I also tried to use the table-extension option and increased its value
 to 10 nm but later the LINCS printed out too many warnings and MD could not
 be done. I know that its not at all a good idea to increase the 1-4 cut off.


 Yup, bad idea. Fix the underlying problem, not the symptoms.

 Mark

 ___
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 http://lists.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 gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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Re: [gmx-users] creating a larger lipid membrane

Amit Choubey wrote:

Hi Justin,

Yes you are right. I didnt fix the periodicity to start with. Could you
tell me how to do that, which command to work with?

Thanks.

Periodicity is corrected using trjconv. This involves creating a .tpr file of
to represent the system and using trjconv -pbc mol -ur compact, or some such
equivalent.

My tutorial gives some information on doing this. Please see:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

-Justin

amit

On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:

Amit Choubey wrote:

Dear Gromacs Users,

I have been trying to generate a larger lipid system but am
running into troubles due to improper initial co-ordinates set
up. Following are the steps i am trying to follow.

1. I start with a 128 dppc membrane and use genconf to create a
larger system. I got the dppc128.pdb from Dr. Peter Tieleman's
website.

Did you correct for periodicity before you extended the system? The
files distributed by Tieleman are compact representations.

2. I changed my topology file accordingly (change the number of
DPPC and Water molecules)

3. I move on to energy minimization. During the mdrun i see the
following message :-

Warning: 1-4 interaction between 1854 and 1857 at distance 6.249
which is larger than the 1-4 table size 2.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Looks to me like two bonded atoms are across the box from each
other, which seems to answer my question above :)

I also notice that the max force does not converge to less than
2000 rather its of the order of 2e+06 .

4. I tried to do energy minimization again on the above system
but the steepest descent could not change the potential energy
substantially and terminated after less that 20 steps. I again
noticed the following warning
Warning: 1-4 interaction between 1854 and 1857 at distance 5.269
which is larger than the 1-4 table size 2.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

5. Now i changed my mdp files to do periodic_molecules = yes .
Note pbc = xyz has been used as default.

Bad idea. This option is for infinite molecules, like nanotubes
or graphene sheets that are supposed to extend across the simulation
box.

Same warnings were printed out during energy minimization.

6. I also tried to use the table-extension option and increased
its value to 10 nm but later the LINCS printed out too many
warnings and MD could not be done. I know that its not at all a
good idea to increase the 1-4 cut off.

The standard advice is to fix the problem with the system, not
change the table-extension.

By the way to be specific the system size was 12 x 12 x 6 in
nm3. I had 256 lipids and about 7300 water molecules.

I believe that this might not be the best way to create a larger

bilayer system. Could somebody suggest me other ways of doing this?

Fix periodicity, then use genconf.

-Justin

Any help will be appreciated thank you

Amit

___
gmx-users mailing listgmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

Re: [gmx-users] creating a larger lipid membrane