[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

[chris . neale]

Hi Steve,

I also use the pull code and would be very interested to more fully  
understand the problem that you are experiencing. However, I don't  
generally modify any code myself, and therefore have no use for your  
private system. What I would be eager to receive is your  
POPC-buckyball system with a small instruction on how I might detect  
the difference between 4.0.3 and 4.0.99 behaviour.


chris.neale |at| utoronto.ca

Chris.

-- original message --

Hi,

The permeants in my bilayer system are improperly pulled in calculations
using all versions of Gromacs 4.0.x including the VERSION
4.0.99_development_20090120.  Since, due to restrictions, I can not
provide the topology file for my system to bugzilla, I constructed a
similar prototypical system using Prof. Tieleman's POPC bilayer
coordinates and field parameters.  A buckyball permenat doped in the
center of this system did indeed react similarly in a 4.0.3 calculation
with an improper pull away from the equilibrated 3.3.1 constraint force
coordinates.  It was heartening to see that this problem was fixed for
that system, by using VERSION 4.0.99_development_20090120.
Unfortunately, again the problem remained for my actual system, even
with use of the newest version of code.

Since the cylinder option is now operational, I have a viable
work-around for this problem.  I am quite appreciative of the attention
that this issue has received.  If there is continued interest, and a
willingness for an engineer to receive the topology file in a less
public forum than bugzilla, I believe we could proceed with the
debugging process.

Thank you,

Steve Fiedler

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Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

[Steve Fiedler]

Hi,

The permeants in my bilayer system are improperly pulled in calculations 
using all versions of Gromacs 4.0.x including the VERSION 
4.0.99_development_20090120.  Since, due to restrictions, I can not 
provide the topology file for my system to bugzilla, I constructed a 
similar prototypical system using Prof. Tieleman's POPC bilayer 
coordinates and field parameters.  A buckyball permenat doped in the 
center of this system did indeed react similarly in a 4.0.3 calculation 
with an improper pull away from the equilibrated 3.3.1 constraint force 
coordinates.  It was heartening to see that this problem was fixed for 
that system, by using VERSION 4.0.99_development_20090120.  
Unfortunately, again the problem remained for my actual system, even 
with use of the newest version of code.


Since the cylinder option is now operational, I have a viable 
work-around for this problem.  I am quite appreciative of the attention 
that this issue has received.  If there is continued interest, and a 
willingness for an engineer to receive the topology file in a less 
public forum than bugzilla, I believe we could proceed with the 
debugging process.


Thank you,

Steve Fiedler




Berk Hess wrote:

Hi,

Just to be sure, the pull code is producing the correct results now?
The only problems should be in several analysis tools.

The analysis tools have been written only with analysis of molecules
or parts of molecules in mind. When you want to analyze groups
that cover two molecules or more there will be pbc problems.
These are not simple to fix. If the distances between all the atoms
in the group are less than half a box length there is a unique COM.
The procedure should be similar to what trjconv -pbc cluster does.

I can try to implement this for g_traj and g_dist.
Are there other tools that cause problems?

Berk

> Date: Mon, 26 Jan 2009 17:46:26 -0500
> From: fied...@umich.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 
4.0.3 regarding pull_geometry=distance

>
> Hi Chris,
>
> Your suggestions were helpful. Due to the nature of this problem, there
> were limitations in the application of the sequence of steps that you
> recommended. Specifically, the difference in the equilibrated structure
> from version 3.3.x to the calculated reference center of mass from
> version 4.0.x causes an unreasonable "jump" with constraint force
> calculation. Resultant bad contacts prohibit generation of a pull
> output file.
>
> More generally though, I believe I understand your broader point: the
> sensitive nature of the periodic box with respect to the pull code and
> possible discrepancies in the pbc treatment by various utilities, may
> cause confusion with the diagnostic process. The test bilayer system I
> created however, centered distantly from the x and y box edges, may
> effectively remove this set of concerns. For example, this
> configuration is relatively unchanged upon "recentering", however it is
> still susceptible to the problem that is the subject of this discussion.
>
> If I can reproduce this phenomenon with a publicly available topology
> file, I can provide the necessary input files for inspection.
>
> Thank you again,
>
> Steve Fiedler
>
>
>
> chris.ne...@utoronto.ca wrote:
> > Hi Steve,
> >
> > what I intended to suggest was actually something different (and much
> > easier).
> >
> > The idea is not that you need some special system to be able to
> > utilize the pull code, but that the pull code is correct whereas the
> > g_dist and g_traj programs are not as good at treating pbc in the way
> > that one desires.
> >
> > I suggest the following.
> >
> > 1. Take your original system and run the pull code for a very short
> > simulation. Use the last line of the output to calculate the relevant
> > displacement
> >
> > 2. Now use trjconv -b -e to get the last frame of the .xtc that
> > resulted from that short MD run as a .gro file, call it final.gro. I
> > suspect that your groups are not entirely in the same simulation box
> > in final.gro.
> >
> > 3. Now make a new .ndx file from that .gro and give it a single
> > residue that is near your binding pocket, call it R_1
> >
> > 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1
> > for centering, call the new .gro file final_center.gro
> >
> > 5. Visualize final_center.gro and ensure that all of your relevant
> > atoms are in the same image in the way that puts the minimum distance
> > between them along a path that is entirely contained within the unit
> > cell. If not, go back to step 3 and try making a group R_2, etc.
> > until this process works. NOTE: you might think that giving trjconv
> > -center the relevant groups that you use for pulling will be a good
> > idea here, but it is not. The problem there is that the atoms may be
> > "centered" by placing half on the left boundary and half on the right
> > boundary. I find using one logically selected residue or atom is the
> > bes

[gmx-users] Re: decoupling charge while maintaining intramolecular potentials

[chris . neale]

Thank you Michael for the detailed reply, I have posted clarifications  
and additional questions or remarks inline below.



Hi, Chris-

I unfortunately can't be too much help, because my free energy
calculations are done through a modified version of Gromacs 3.1.4, and
I am currently working with Berk and Erik to get the important
modifications into the 4.0 branch.


I am a new user of the free energy code. I am somewhat confused
regarding the method that should be applied to decouple the long range
interactions of the solvent from the solute while still maintaining
intramolecular long-range interactions for the solute.


By long range interactions, you mean the ones outside the cutoff,
correct?  Because there's another set of difficulties dealing with the
ones that are shortange nonbonded interactions as well.  Could you
clarify?


When I said "long-range" I should have said "non-bonded" instead  
throughout this entire document. Sorry for the incorrect terminology.  
Therefore I am under the impression that one wants to decouple the  
intermolecular solvent-solute nonbonded interactions without affecting  
any intramolecular nonbonded interactions. I have seen this applied in  
your papers and some others, many of them done via charmm.





I was able to find some information in this thread:
http://www.gromacs.org/pipermail/gmx-developers/2006-January/001498.html
but it is still unclear to me.


I'm not surprised, it was unclear for us at the time as well :)


I have reproduced the methane and tip3p energies of solvation based on
the tutorial that is on the gromacs wiki. In this case, I simply
assigned new charge values of 0 in the B state without making any
special considerations for intramolecular O-H values. However, tip3p
is rigid and perhaps maintaining the intramolecular q-q and LJ
components is not essential in this case.


This is where I get confused -- are you talking about long range, or
any intramolecule interactions.  Certainly for methane and tip3p,
there aren't any, because all atoms are 1,3 neighbors.


I am talking about any nonbonded intramolecular interactions. Further,  
your point regarding 1-2 and 1-3 interactions is well taken. My  
molecule of interest is a dodecylphosphocholine detergent and  
therefore there will be substantial intramolecular nonbonded  
interactions that I believe it would be best to maintain.





1. Is it necessary to maintain the intramolecular long-range
interactions for the solute while decoupling LJ or charge? If not
absolutely required, does it affect the rate of convergence?


If you change the intramolecular nonbonded interactions, then you
would have to perform a second vacuum calculation in which you turn
them back on.   In terms of rates of convergence -- nobody really
knows.  If it's a intramolecular hydrogen bonding system, then turning
off the intramolecular interactions might be faster.


What I am actually doing is annihilating one DPC detergent from a DPC  
micelle and, separately, annihilating one DPC detergent monomer from  
bulk water. The dG(monomer) minus dG(micelle) should then be related  
to the relative probabilities of monomeric and aggregated states. I  
have left out the monomer restraints and the volume correction here  
for simpicity. It is my impression that this monomer-in-bulk  
annihilation provides the second simulation that you mentioned above,  
although I will still require this second simulation even if I  
maintain my intramolecular non-bonded interactions since I am  
interested in the relative probabilities of the monomeric and  
aggregated state, both in solution, and not in solvation free energies.


The reason that I thought one would want to not change the  
intramolecular interactions is that it seems to me that this will make  
the d(pot)d(lambda) energies larger and then subtracting 200-190=10  
seems like it will have more uncertainty than if the dvdl integrated  
energies were all smaller. This is just based on the idea that a small  
difference of two large numbers is often difficult to obtain precisely.


However, I see your point about relatively stable intramolecular  
interactions. I will need to think further about that one.





2. Is this already handled by the free-energy code?


I can't speak for the 4.0 code.  Berk was introducing nonbonded pair
terms such that these pair terms would overrule the 'alchemical'
transformation, resulting in unchanged intramolelcular nonbonded
interactions.  I actually don't know the current state of this change,
though.


3. If not, how might one go about doing this? My confusion with some
additional [ pairs ] entry is how gromacs would get the right
combination for lambda=0 and lambda=1 (not to mention intermediate
states).


I'm a bit confused.  I would think that you would just want to set
them to the lambda=0 state, so that intramolecular interactions were
preserved.  Am I thinking of something different than you are?


If you're just talking about how to handle

[gmx-users] Re: decoupling charge while maintaining intramolecular potentials (chris.ne...@utoronto.ca)

[Michael Shirts]

Hi, Chris-

I unfortunately can't be too much help, because my free energy
calculations are done through a modified version of Gromacs 3.1.4, and
I am currently working with Berk and Erik to get the important
modifications into the 4.0 branch.

> I am a new user of the free energy code. I am somewhat confused
> regarding the method that should be applied to decouple the long range
> interactions of the solvent from the solute while still maintaining
> intramolecular long-range interactions for the solute.

By long range interactions, you mean the ones outside the cutoff,
correct?  Because there's another set of difficulties dealing with the
ones that are shortange nonbonded interactions as well.  Could you
clarify?

> I was able to find some information in this thread:
> http://www.gromacs.org/pipermail/gmx-developers/2006-January/001498.html
> but it is still unclear to me.

I'm not surprised, it was unclear for us at the time as well :)

> I have reproduced the methane and tip3p energies of solvation based on
> the tutorial that is on the gromacs wiki. In this case, I simply
> assigned new charge values of 0 in the B state without making any
> special considerations for intramolecular O-H values. However, tip3p
> is rigid and perhaps maintaining the intramolecular q-q and LJ
> components is not essential in this case.

This is where I get confused -- are you talking about long range, or
any intramolecule interactions.  Certainly for methane and tip3p,
there aren't any, because all atoms are 1,3 neighbors.

> 1. Is it necessary to maintain the intramolecular long-range
> interactions for the solute while decoupling LJ or charge? If not
> absolutely required, does it affect the rate of convergence?

If you change the intramolecular nonbonded interactions, then you
would have to perform a second vacuum calculation in which you turn
them back on.   In terms of rates of convergence -- nobody really
knows.  If it's a intramolecular hydrogen bonding system, then turning
off the intramolecular interactions might be faster.

> 2. Is this already handled by the free-energy code?

I can't speak for the 4.0 code.  Berk was introducing nonbonded pair
terms such that these pair terms would overrule the 'alchemical'
transformation, resulting in unchanged intramolelcular nonbonded
interactions.  I actually don't know the current state of this change,
though.

> 3. If not, how might one go about doing this? My confusion with some
> additional [ pairs ] entry is how gromacs would get the right
> combination for lambda=0 and lambda=1 (not to mention intermediate
> states).

I'm a bit confused.  I would think that you would just want to set
them to the lambda=0 state, so that intramolecular interactions were
preserved.  Am I thinking of something different than you are?

Best,
Michael

~~~

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shi...@virginia.edu
(434)-243-1821
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Re: [gmx-users] the wanging: atom names don't match in top and gro file

[Justin A. Lemkul]

He, Yang wrote:

Hi Mark,

You mean my format in the .GRO file is not very correct. What do you mean by saying 
" the second column one
too far to the right." ?



Yes, your structure file seems mangled.  For .gro format specifications:

http://www.gromacs.org/documentation/reference_4.0/online/gro.html

-Justin


Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Tuesday, January 27, 2009 5:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the wanging: atom names don't match in top and gro 
file

He, Yang wrote:

Hi all users,

when I run the command grompp , it always shows that

processing coordinates...
Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (C13 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C14 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (N15 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (N16 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q17 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q18 - Q1)
 Warning: atom names in DNA.top and DNA.gro don't match (C19 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C20 - C2)
 Warning: atom names in DNA.top and DNA.gro don't match (N21 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (N22 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
WARNING 1 [file "DNA.top", line 12]:
  17 non-matching atom names
  atom names from DNA.top will be used
  atom names from DNA.gro will be ignored

I have checked that for some times but the warning is still on. I will list the 
content below:
 for .GRO FILE
1DNA N10  10   0.668430  0.387405  6.709000
1DNA Q11  11  -5.736999  6.827887  5.566000
1DNA Q12  12   8.266537 -3.346277  4.574000
1DNA C13  13  -1.947247  6.703736  4.66
1DNA C14  14   5.773899 -3.923511  2.10
1DNA N15  15   0.161888  0.755429  3.431000
1DNA N16  16   1.506403 -1.802878  3.189000
1DNA Q17  17  -0.627998  8.896000  2.186000
1DNA Q18  18   4.720877 -7.566143  1.194000
1DNA C19  19   2.365001  6.568000  1.28
1DNA C20  20   2.365001 -6.568000 -1.28
1DNA N21  21   0.159001  2.344000  0.191000
1DNA N22  22   0.575000 -0.516000 -0.051000


If the .gro format is fixed-format, then you have the second column one
too far to the right.


FOR itp file

  10Nda  1 DNA  N10   10   0
  11Qa   1 DNA  Q11   11 -1.0
  12Qa   1 DNA  Q12   12 -1.0
  13C1 DNA  C13   13   0
  14C1 DNA  C14   14   0
  15Nda  1 DNA  N15   15   0
  16Nda  1 DNA  N16   16   0
  17Qa   1 DNA  Q17   17 -1.0
  18Qa   1 DNA  Q18   18 -1.0
  19C1 DNA  C19   19   0
  20C1 DNA  C20   20   0
  21Nda  1 DNA  N21   21   0
  22Nda  1 DNA  N22   22   0

Any suggestions will be appreciated .

Regards,

Yang
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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech

RE: [gmx-users] the wanging: atom names don't match in top and gro file

[He, Yang]

Hi Mark,

You mean my format in the .GRO file is not very correct. What do you mean by 
saying " the second column one
too far to the right." ?

Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Tuesday, January 27, 2009 5:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the wanging: atom names don't match in top and gro 
file

He, Yang wrote:
> Hi all users,
>
> when I run the command grompp , it always shows that
>
> processing coordinates...
> Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (C13 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (C14 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (N15 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (N16 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q17 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q18 - Q1)
>  Warning: atom names in DNA.top and DNA.gro don't match (C19 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (C20 - C2)
>  Warning: atom names in DNA.top and DNA.gro don't match (N21 - N2)
> Warning: atom names in DNA.top and DNA.gro don't match (N22 - N2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> WARNING 1 [file "DNA.top", line 12]:
>   17 non-matching atom names
>   atom names from DNA.top will be used
>   atom names from DNA.gro will be ignored
>
> I have checked that for some times but the warning is still on. I will list 
> the content below:
>  for .GRO FILE
> 1DNA N10  10   0.668430  0.387405  6.709000
> 1DNA Q11  11  -5.736999  6.827887  5.566000
> 1DNA Q12  12   8.266537 -3.346277  4.574000
> 1DNA C13  13  -1.947247  6.703736  4.66
> 1DNA C14  14   5.773899 -3.923511  2.10
> 1DNA N15  15   0.161888  0.755429  3.431000
> 1DNA N16  16   1.506403 -1.802878  3.189000
> 1DNA Q17  17  -0.627998  8.896000  2.186000
> 1DNA Q18  18   4.720877 -7.566143  1.194000
> 1DNA C19  19   2.365001  6.568000  1.28
> 1DNA C20  20   2.365001 -6.568000 -1.28
> 1DNA N21  21   0.159001  2.344000  0.191000
> 1DNA N22  22   0.575000 -0.516000 -0.051000

If the .gro format is fixed-format, then you have the second column one
too far to the right.

> FOR itp file
>
>   10Nda  1 DNA  N10   10   0
>   11Qa   1 DNA  Q11   11 -1.0
>   12Qa   1 DNA  Q12   12 -1.0
>   13C1 DNA  C13   13   0
>   14C1 DNA  C14   14   0
>   15Nda  1 DNA  N15   15   0
>   16Nda  1 DNA  N16   16   0
>   17Qa   1 DNA  Q17   17 -1.0
>   18Qa   1 DNA  Q18   18 -1.0
>   19C1 DNA  C19   19   0
>   20C1 DNA  C20   20   0
>   21Nda  1 DNA  N21   21   0
>   22Nda  1 DNA  N22   22   0
>
> Any suggestions will be appreciated .
>
> Regards,
>
> Yang
> ___
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Re: [gmx-users] the wanging: atom names don't match in top and gro file

[Mark Abraham]

He, Yang wrote:

Hi all users,

when I run the command grompp , it always shows that

processing coordinates...
Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (C13 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C14 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (N15 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (N16 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q17 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q18 - Q1)
 Warning: atom names in DNA.top and DNA.gro don't match (C19 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C20 - C2)
 Warning: atom names in DNA.top and DNA.gro don't match (N21 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (N22 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
WARNING 1 [file "DNA.top", line 12]:
  17 non-matching atom names
  atom names from DNA.top will be used
  atom names from DNA.gro will be ignored

I have checked that for some times but the warning is still on. I will list the 
content below:
 for .GRO FILE
1DNA N10  10   0.668430  0.387405  6.709000
1DNA Q11  11  -5.736999  6.827887  5.566000
1DNA Q12  12   8.266537 -3.346277  4.574000
1DNA C13  13  -1.947247  6.703736  4.66
1DNA C14  14   5.773899 -3.923511  2.10
1DNA N15  15   0.161888  0.755429  3.431000
1DNA N16  16   1.506403 -1.802878  3.189000
1DNA Q17  17  -0.627998  8.896000  2.186000
1DNA Q18  18   4.720877 -7.566143  1.194000
1DNA C19  19   2.365001  6.568000  1.28
1DNA C20  20   2.365001 -6.568000 -1.28
1DNA N21  21   0.159001  2.344000  0.191000
1DNA N22  22   0.575000 -0.516000 -0.051000


If the .gro format is fixed-format, then you have the second column one 
too far to the right.



FOR itp file

  10Nda  1 DNA  N10   10   0
  11Qa   1 DNA  Q11   11 -1.0
  12Qa   1 DNA  Q12   12 -1.0
  13C1 DNA  C13   13   0
  14C1 DNA  C14   14   0
  15Nda  1 DNA  N15   15   0
  16Nda  1 DNA  N16   16   0
  17Qa   1 DNA  Q17   17 -1.0
  18Qa   1 DNA  Q18   18 -1.0
  19C1 DNA  C19   19   0
  20C1 DNA  C20   20   0
  21Nda  1 DNA  N21   21   0
  22Nda  1 DNA  N22   22   0

Any suggestions will be appreciated .

Regards,

Yang
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[gmx-users] the wanging: atom names don't match in top and gro file

[He, Yang]

Hi all users,

when I run the command grompp , it always shows that

processing coordinates...
Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (C13 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C14 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (N15 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (N16 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q17 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q18 - Q1)
 Warning: atom names in DNA.top and DNA.gro don't match (C19 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C20 - C2)
 Warning: atom names in DNA.top and DNA.gro don't match (N21 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (N22 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
WARNING 1 [file "DNA.top", line 12]:
  17 non-matching atom names
  atom names from DNA.top will be used
  atom names from DNA.gro will be ignored

I have checked that for some times but the warning is still on. I will list the 
content below:
 for .GRO FILE
1DNA N10  10   0.668430  0.387405  6.709000
1DNA Q11  11  -5.736999  6.827887  5.566000
1DNA Q12  12   8.266537 -3.346277  4.574000
1DNA C13  13  -1.947247  6.703736  4.66
1DNA C14  14   5.773899 -3.923511  2.10
1DNA N15  15   0.161888  0.755429  3.431000
1DNA N16  16   1.506403 -1.802878  3.189000
1DNA Q17  17  -0.627998  8.896000  2.186000
1DNA Q18  18   4.720877 -7.566143  1.194000
1DNA C19  19   2.365001  6.568000  1.28
1DNA C20  20   2.365001 -6.568000 -1.28
1DNA N21  21   0.159001  2.344000  0.191000
1DNA N22  22   0.575000 -0.516000 -0.051000

FOR itp file

  10Nda  1 DNA  N10   10   0
  11Qa   1 DNA  Q11   11 -1.0
  12Qa   1 DNA  Q12   12 -1.0
  13C1 DNA  C13   13   0
  14C1 DNA  C14   14   0
  15Nda  1 DNA  N15   15   0
  16Nda  1 DNA  N16   16   0
  17Qa   1 DNA  Q17   17 -1.0
  18Qa   1 DNA  Q18   18 -1.0
  19C1 DNA  C19   19   0
  20C1 DNA  C20   20   0
  21Nda  1 DNA  N21   21   0
  22Nda  1 DNA  N22   22   0

Any suggestions will be appreciated .

Regards,

Yang
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[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.

[Chris Neale]

Hello,

when applying the free energy code, I expected that the instantaneous 
energy of a given conformation when free_energy = yes & init_lambda = 
0.00 would be identical to that when free_energy = no. However, I have 
found this not to be the case in zero-step mdrun. This is the same 
result that I get from gmx v 3.3.1, 3.3.3, and 4.0.3. Is this expected?


With free_energy = yes & init_lambda = 0.00:
Coulomb (SR)-3.23064e+05

With free_energy = no:
Coulomb (SR)-3.22654e+05

and all other energy components are identical. The Coulomb (SR) 
difference seems significant to me. Note that the free_energy = no 
values are identical to those that I get when I use a topology that has 
not been modified to add a B-state so I don't think that my A-state 
values are incorrect.


## free_energy related .mdp options:
free_energy  = yes
init_lambda  = 0.00
delta_lambda = 0
sc_alpha =0.0
sc-power =1.0
sc-sigma = 0.3

## Other .mdp options:
nsteps  = 0
tinit   =  0
dt  =  0.004
integrator  =  sd
comm_mode   =  linear
nstcomm =  1
comm_grps   =  System
nstlog  =  2500
nstlist =  5
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rcoulomb=  0.9
fourierspacing  =  0.12
pme_order   =  4
vdwtype =  cut-off
rvdw_switch =  0
rvdw=  1.4
rlist   =  0.9
DispCorr=  EnerPres
Pcoupl  =  Berendsen
pcoupltype  =  isotropic
compressibility =  4.5e-5
ref_p   =  1.
tau_p   =  4.0
tcoupl  =  Berendsen
tc_grps =  System
tau_t   =  0.1   
ref_t   =  300.  
annealing   =  no

gen_vel =  no
unconstrained-start =  yes
gen_temp=  300.
gen_seed=  9896
constraints =  all-bonds
constraint_algorithm=  lincs
lincs-iter  =  1
lincs-order =  6


Thank you,
Chris.
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Re: [gmx-users] ligand-protein distance restraint

[Mark Abraham]

Pathumwadee Intharathep wrote:

Dear Mark,
 
I tried to make a hybrid [moleculetype] section that includes one 
protein and 4 ligands, it is very complicate way to do.
 
I have to do mannaully to put [atoms], [bonds], [pairs], 
[angles] and [dihedral] for each ligand and need to re-number for all, 
if not, the error of "Atoms in the .top are not numbered consecutively 
from 1" will be occured.
Do you have any more esier way to make a hybrid [moleculetype] ? 


No. It is fiddly, but from your starting ligand [moleculetype] you copy 
and paste before adding the same integer to each atom number to generate 
a ligand in the hybrid. You may find it easier to write a shell script 
to do this.


There's also the advice I gave on Monday in another thread 
http://www.gromacs.org/pipermail/gmx-users/2009-January/a.html


Depending how you generated your initial topologies, it may be easier to 
use that tool on the whole assembly - with a force field other than ffgmx.


Mark
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[gmx-users] ligand-protein distance restraint

[Pathumwadee Intharathep]

Dear Mark,
 
I tried to make a hybrid [moleculetype] section that includes one protein and 4 
ligands, it is very complicate way to do.
 
I have to do mannaully to put [atoms], [bonds], [pairs], 
[angles] and [dihedral] for each ligand and need to re-number for all, if 
not, the error of "Atoms in the .top are not numbered consecutively from 
1" will be occured.
Do you have any more esier way to make a hybrid [moleculetype] ? 
 
Beast regards,
 
pathum


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[gmx-users] Rosetta Academic Training Workshop

[Nir London]

Due to public demand, “Rosetta Design Group” is organizing a “Rosetta”  
software training workshop, aimed for academic groups. The format of  
the workshop will be a “webinar” - a web seminar, enabling more groups  
to attend while avoiding the annoying jet lag and accommodation  
troubles. Would you be interested in participating? If so please fill  
the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ 
 and we will contact you when the details are finalized.*


Nir London | Rosetta Design Group
http://rosettadesigngroup.com/

* If you’re not from an academic group, don’t worry, write us anyway…

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Re: [gmx-users] Segmentation fault with genbox -nmol (version 4.0.3)

[David van der Spoel]

Berk Hess wrote:



 > Date: Tue, 27 Jan 2009 08:46:35 +0100
 > From: sp...@xray.bmc.uu.se
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Segmentation fault with genbox -nmol 
(version 4.0.3)

 >
 > Justin A. Lemkul wrote:
 > >
 > > Hi All,
 > >
 > > I'm building a system consisting of a protein complex with a few 
ligands

 > > free in solution at the outset of the simulation. I'm using genbox -ci
 > > -nmol to insert the ligands prior to solvation. I'm using version 
4.0.3

 > > on a dual-core Intel MacBook. The following command fails:
 > >
 > > genbox -cp complex_newbox.gro -ci lig.gro -nmol 10
 > >
 > > The command works, however, for values of -nmol < 4. The command with
 > > -nmol 10 works on another machine, an AMD64 Ubuntu box, so this 
problem

 > > appears specific to my Mac. Using genbox from version 3.3.3 works just
 > > fine on the MacBook, and both 4.0.3 and 3.3.3 were built using the 
same

 > > compilers (gcc suite, version 4.0.1).
 > >
 > > The last few lines of genbox.log from -debug 1 are:
 > >
 > > No fcdata or table file name passed, can not read table, can not do
 > > bonded interactions
 > > Going to determine what solvent types we have.
 > >
 > > ...in case that's helpful. Any ideas why this may have broken, or why
 > > it may be specific to my Mac?
 > >
 > >
 > > Thanks,
 > > Justin
 > >
 > please enter a bugzilla for this.

I just ran valgrind on genbox 4.0.4_pre.
I get a uninit value warning in check_solvent_cg.
I fixed two issues in this part of the code, so it could be that
4.0.4 has less problems than 4.0.3.
But looking at do_nsgrid it seems that genbox still does not
calculate overlap between the inserted molecules,
although the output says it does.

What does genbox do?


Drag around a lot of history.

There is also a problem with vsites, waters are put in place of vsites 
but this could be due to other problems (archaic gromos-centric input 
files).




Berk

 >
 > --
 > David van der Spoel, Ph.D., Professor of Biology
 > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
 > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
 > ___
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 > Please search the archive at http://www.gromacs.org/search before 
posting!

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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

[Berk Hess]

Hi,

I think g_clustsize requires a different algorithm.
Here you don't know a priori what the group is.
I guess things are easier here, since you always cluster
(parts of) molecules. Or am I wrong?

I am not familiar with this program.
If there are problems, please file a bugzilla.

Berk

Date: Tue, 27 Jan 2009 09:58:32 +0100
From: r.fried...@bioc.uzh.ch
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to  4.0.3   
regarding pull_geometry=distance






  


Dear Berk,



I think that g_clustsize has a similar problem. IIRC I fixed it in a
similar way on my own copy.

There are probably other tools that will suffer from this as well, but
for g_clustsize it's important because it may deal with such groups.



Same goes for trjconv, e.g., for a protein and ligand. 



Ran.



Berk Hess wrote:

  Hi,

  

Just to be sure, the pull code is producing the correct results now?

The only problems should be in several analysis tools.

  

The analysis tools have been written only with analysis of molecules

or parts of molecules in mind. When you want to analyze groups

that cover two molecules or more there will be pbc problems.

These are not simple to fix. If the distances between all the atoms

in the group are less than half a box length there is a unique COM.

The procedure should be similar to what trjconv -pbc cluster does.

  

I can try to implement this for g_traj and g_dist.

Are there other tools that cause problems?

  

Berk

  

> Date: Mon, 26 Jan 2009 17:46:26 -0500

> From: fied...@umich.edu

> To: gmx-users@gromacs.org

> Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to
4.0.3 regarding pull_geometry=distance

> 

> Hi Chris,

> 

> Your suggestions were helpful. Due to the nature of this problem,
there 

> were limitations in the application of the sequence of steps that
you 

> recommended. Specifically, the difference in the equilibrated
structure 

> from version 3.3.x to the calculated reference center of mass from
  

> version 4.0.x causes an unreasonable "jump" with constraint force 

> calculation. Resultant bad contacts prohibit generation of a pull 

> output file.

> 

> More generally though, I believe I understand your broader point:
the 

> sensitive nature of the periodic box with respect to the pull code
and 

> possible discrepancies in the pbc treatment by various utilities,
may 

> cause confusion with the diagnostic process. The test bilayer
system I 

> created however, centered distantly from the x and y box edges,
may 

> effectively remove this set of concerns. For example, this 

> configuration is relatively unchanged upon "recentering", however
it is 

> still susceptible to the problem that is the subject of this
discussion.

> 

> If I can reproduce this phenomenon with a publicly available
topology 

> file, I can provide the necessary input files for inspection.

> 

> Thank you again,

> 

> Steve Fiedler

> 

> 

> 

> chris.ne...@utoronto.ca wrote:

> > Hi Steve,

> >

> > what I intended to suggest was actually something different
(and much 

> > easier).

> >

> > The idea is not that you need some special system to be able
to 

> > utilize the pull code, but that the pull code is correct
whereas the 

> > g_dist and g_traj programs are not as good at treating pbc in
the way 

> > that one desires.

> >

> > I suggest the following.

> >

> > 1. Take your original system and run the pull code for a very
short 

> > simulation. Use the last line of the output to calculate the
relevant 

> > displacement

> >

> > 2. Now use trjconv -b -e to get the last frame of the .xtc
that 

> > resulted from that short MD run as a .gro file, call it
final.gro. I 

> > suspect that your groups are not entirely in the same
simulation box 

> > in final.gro.

> >

> > 3. Now make a new .ndx file from that .gro and give it a
single 

> > residue that is near your binding pocket, call it R_1

> >

> > 4. Now apply trjconv -center -pbc mol -ur compact while
selecting R_1 

> > for centering, call the new .gro file final_center.gro

> >

> > 5. Visualize final_center.gro and ensure that all of your
relevant 

> > atoms are in the same image in the way that puts the minimum
distance 

> > between them along a path that is entirely contained within
the unit 

> > cell. If not, go back to step 3 and try making a group R_2,
etc. 

> > until this process works. NOTE: you might think that giving
trjconv 

> > -center the relevant groups that you use for pulling will be
a good 

> > idea here, but it is not. The problem there is that the atoms
may be 

> > "centered" by placing half on the left boundary and half on
the right 

> > boundary. I find using one logically selected residue or atom
is the 

> > best method here.

> >

> > 6. Assuming that you got what you wanted in step 5, now run
g_traj and 

> > g_dist on final_center.gro. In my case, I found that g_traj
and g_dist 

> > give the same answer as the pull code out

RE: [gmx-users] Segmentation fault with genbox -nmol (version 4.0.3)

[Berk Hess]

> Date: Tue, 27 Jan 2009 08:46:35 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Segmentation fault with genbox -nmol (version 4.0.3)
> 
> Justin A. Lemkul wrote:
> > 
> > Hi All,
> > 
> > I'm building a system consisting of a protein complex with a few ligands 
> > free in solution at the outset of the simulation.  I'm using genbox -ci 
> > -nmol to insert the ligands prior to solvation.  I'm using version 4.0.3 
> > on a dual-core Intel MacBook.  The following command fails:
> > 
> > genbox -cp complex_newbox.gro -ci lig.gro -nmol 10
> > 
> > The command works, however, for values of -nmol < 4.  The command with 
> > -nmol 10 works on another machine, an AMD64 Ubuntu box, so this problem 
> > appears specific to my Mac.  Using genbox from version 3.3.3 works just 
> > fine on the MacBook, and both 4.0.3 and 3.3.3 were built using the same 
> > compilers (gcc suite, version 4.0.1).
> > 
> > The last few lines of genbox.log from -debug 1 are:
> > 
> > No fcdata or table file name passed, can not read table, can not do 
> > bonded interactions
> > Going to determine what solvent types we have.
> > 
> > ...in case that's helpful.  Any ideas why this may have broken, or why 
> > it may be specific to my Mac?
> > 
> > 
> > Thanks,
> > Justin
> > 
> please enter a bugzilla for this.

I just ran valgrind on genbox 4.0.4_pre.
I get a uninit value warning in check_solvent_cg.
I fixed two issues in this part of the code, so it could be that
4.0.4 has less problems than 4.0.3.
But looking at do_nsgrid it seems that genbox still does not
calculate overlap between the inserted molecules,
although the output says it does.

What does genbox do?

Berk

> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
> ___
> 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 gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

[Ran Friedman]

Dear Berk,

I think that g_clustsize has a similar problem. IIRC I fixed it in a
similar way on my own copy.
There are probably other tools that will suffer from this as well, but
for g_clustsize it's important because it may deal with such groups.

Same goes for trjconv, e.g., for a protein and ligand.

Ran.

Berk Hess wrote:
> Hi,
>
> Just to be sure, the pull code is producing the correct results now?
> The only problems should be in several analysis tools.
>
> The analysis tools have been written only with analysis of molecules
> or parts of molecules in mind. When you want to analyze groups
> that cover two molecules or more there will be pbc problems.
> These are not simple to fix. If the distances between all the atoms
> in the group are less than half a box length there is a unique COM.
> The procedure should be similar to what trjconv -pbc cluster does.
>
> I can try to implement this for g_traj and g_dist.
> Are there other tools that cause problems?
>
> Berk
>
> > Date: Mon, 26 Jan 2009 17:46:26 -0500
> > From: fied...@umich.edu
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to
> 4.0.3 regarding pull_geometry=distance
> >
> > Hi Chris,
> >
> > Your suggestions were helpful. Due to the nature of this problem, there
> > were limitations in the application of the sequence of steps that you
> > recommended. Specifically, the difference in the equilibrated structure
> > from version 3.3.x to the calculated reference center of mass from
> > version 4.0.x causes an unreasonable "jump" with constraint force
> > calculation. Resultant bad contacts prohibit generation of a pull
> > output file.
> >
> > More generally though, I believe I understand your broader point: the
> > sensitive nature of the periodic box with respect to the pull code and
> > possible discrepancies in the pbc treatment by various utilities, may
> > cause confusion with the diagnostic process. The test bilayer system I
> > created however, centered distantly from the x and y box edges, may
> > effectively remove this set of concerns. For example, this
> > configuration is relatively unchanged upon "recentering", however it is
> > still susceptible to the problem that is the subject of this discussion.
> >
> > If I can reproduce this phenomenon with a publicly available topology
> > file, I can provide the necessary input files for inspection.
> >
> > Thank you again,
> >
> > Steve Fiedler
> >
> >
> >
> > chris.ne...@utoronto.ca wrote:
> > > Hi Steve,
> > >
> > > what I intended to suggest was actually something different (and much
> > > easier).
> > >
> > > The idea is not that you need some special system to be able to
> > > utilize the pull code, but that the pull code is correct whereas the
> > > g_dist and g_traj programs are not as good at treating pbc in the way
> > > that one desires.
> > >
> > > I suggest the following.
> > >
> > > 1. Take your original system and run the pull code for a very short
> > > simulation. Use the last line of the output to calculate the relevant
> > > displacement
> > >
> > > 2. Now use trjconv -b -e to get the last frame of the .xtc that
> > > resulted from that short MD run as a .gro file, call it final.gro. I
> > > suspect that your groups are not entirely in the same simulation box
> > > in final.gro.
> > >
> > > 3. Now make a new .ndx file from that .gro and give it a single
> > > residue that is near your binding pocket, call it R_1
> > >
> > > 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1
> > > for centering, call the new .gro file final_center.gro
> > >
> > > 5. Visualize final_center.gro and ensure that all of your relevant
> > > atoms are in the same image in the way that puts the minimum distance
> > > between them along a path that is entirely contained within the unit
> > > cell. If not, go back to step 3 and try making a group R_2, etc.
> > > until this process works. NOTE: you might think that giving trjconv
> > > -center the relevant groups that you use for pulling will be a good
> > > idea here, but it is not. The problem there is that the atoms may be
> > > "centered" by placing half on the left boundary and half on the right
> > > boundary. I find using one logically selected residue or atom is the
> > > best method here.
> > >
> > > 6. Assuming that you got what you wanted in step 5, now run g_traj
> and
> > > g_dist on final_center.gro. In my case, I found that g_traj and
> g_dist
> > > give the same answer as the pull code output when I am using
> > > final_center.gro, but not always when I am using final.gro.
> > >
> > > *** I always laugh when these problems arise because, in an important
> > > sense, the protein *did* jump out of the simulation box... at
> least as
> > > far as g_traj and g_dist are concerned. This, we must hope, is
> > > correctly treated in the pull code even though it is incorrectly (or
> > > at least unintuitively) treated by g_traj and g_dist.
> > >
> > > Chris.
> > >
> > > -- o

Re: [gmx-users] restore pbc after a rotation

[XAvier Periole]

Hi Tsjerk,

There is no rush and I really can use the copies of the box.

But as you insist I'll send you the gro file off list.

XAvier.

On Jan 26, 2009, at 9:06 PM, Tsjerk Wassenaar wrote:


Hi Xavier,

By when do you need it? You can send me one frame ( .gro) and I can
see what I can do. But no guarantees, and no time indication :(

Cheers,

Tsjerk

On Mon, Jan 26, 2009 at 7:11 PM, XAvier Periole   
wrote:


On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote:


Hi XAvier,

Unfortunately, you're out of luck. The coordinates do not contain
information regarding the proper orientation with respect to the
coordinate system.


No they don't.

May be I should have mentioned that I know for each
conformation of the system (protein embedded in a membrane
bilayer) the exact transformation that has been that has
been operated: a rotation around the z axis.


That's the short answer. I guess you did save all atoms, at least of
proteins and lipids, in which case you could do a search for a
rotation matrix  that restores your PBC. If you have a brick or
triclinic representation of your atoms the easiest solution is to  
fit

planes through the sides, from which you can infer the original
coordinate system. Then you can rotate that back to match the one
stored.


The other option I found is to duplicate the system on x and y
directions, then center a copy of the protein and finally put  
everything

inside the new cell (made up from 4 copies of the original cell).
Then when rotating the pbc and included on the x and y directions.

Thanks for you thoughts I knew you'd had but I hope for a magic
solution.

Best,
XAvier


Hope it helps,

Tsjerk

On Sun, Jan 25, 2009 at 7:43 PM, XAvier Periole   
wrote:


Dears,

I need to rerun a trajectory that has been rotated to orient a  
molecule

according to a reference. The pbc are therefore broken.

Would anyone know how to restore the correct position of the  
atoms inside
the unit cell after the rotation is applied. The rotation is  
actually

applied around
only one axis (z, membrane normal).

Thanks for any suggestion.
XAvier.

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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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--
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] Software inconsistency error.

[Berk Hess]

Hi,

This problem has been fixed in 4.0.3
Please upgrade to 4.0.3.

Berk

> From: haziz...@razi.tums.ac.ir
> To: gmx-users@gromacs.org
> Date: Tue, 27 Jan 2009 11:07:03 +0330
> Subject: [gmx-users] Software inconsistency error.
> 
> Hi
> I want to have cg minimization after steep minimization of my MD result .
> but every time this error appeare. 
> 
> < Source code file: minimize.c, line: 404
> 
> Software inconsistency error:
> state mismatch in do_em_step>>
> 
> What could be the reason ?
> Thanks.
> 
> 
> 
> 
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
> 
> 
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
> 
> ___
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RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

[Berk Hess]

Hi,

Just to be sure, the pull code is producing the correct results now?
The only problems should be in several analysis tools.

The analysis tools have been written only with analysis of molecules
or parts of molecules in mind. When you want to analyze groups
that cover two molecules or more there will be pbc problems.
These are not simple to fix. If the distances between all the atoms
in the group are less than half a box length there is a unique COM.
The procedure should be similar to what trjconv -pbc cluster does.

I can try to implement this for g_traj and g_dist.
Are there other tools that cause problems?

Berk

> Date: Mon, 26 Jan 2009 17:46:26 -0500
> From: fied...@umich.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to4.0.3   
> regarding pull_geometry=distance
> 
> Hi Chris,
> 
> Your suggestions were helpful.  Due to the nature of this problem, there 
> were limitations in the application of the sequence of steps that you 
> recommended.  Specifically, the difference in the equilibrated structure 
> from version 3.3.x to the calculated reference center of mass from 
> version 4.0.x causes an unreasonable "jump" with constraint force 
> calculation.  Resultant bad contacts prohibit generation of a pull 
> output file.
> 
> More generally though, I believe I understand your broader point: the 
> sensitive nature of the periodic box with respect to the pull code and 
> possible discrepancies in the pbc treatment by various utilities, may 
> cause confusion with the diagnostic process.   The test bilayer system I 
> created however, centered distantly from the x and y box edges, may 
> effectively remove this set of concerns.  For example, this 
> configuration is relatively unchanged upon "recentering", however it is 
> still susceptible to the problem that is the subject of this discussion.
> 
> If I can reproduce this phenomenon with a publicly available topology 
> file, I can provide the necessary input files for inspection.
> 
> Thank you again,
> 
> Steve Fiedler
> 
> 
> 
> chris.ne...@utoronto.ca wrote:
> > Hi Steve,
> >
> > what I intended to suggest was actually something different (and much 
> > easier).
> >
> > The idea is not that you need some special system to be able to 
> > utilize the pull code, but that the pull code is correct whereas the 
> > g_dist and g_traj programs are not as good at treating pbc in the way 
> > that one desires.
> >
> > I suggest the following.
> >
> > 1. Take your original system and run the pull code for a very short 
> > simulation. Use the last line of the output to calculate the relevant 
> > displacement
> >
> > 2. Now use trjconv -b -e to get the last frame of the .xtc that 
> > resulted from that short MD run as a .gro file, call it final.gro. I 
> > suspect that your groups are not entirely in the same simulation box 
> > in final.gro.
> >
> > 3. Now make a new .ndx file from that .gro and give it a single 
> > residue that is near your binding pocket, call it R_1
> >
> > 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 
> > for centering, call the new .gro file final_center.gro
> >
> > 5. Visualize final_center.gro and ensure that all of your relevant 
> > atoms are in the same image in the way that puts the minimum distance 
> > between them along a path that is entirely contained within the unit 
> > cell. If not, go back to step 3 and try making a group R_2, etc.  
> > until this process works. NOTE: you might think that giving trjconv 
> > -center the relevant groups that you use for pulling will be a good 
> > idea here, but it is not. The problem there is that the atoms may be 
> > "centered" by placing half on the left boundary and half on the right 
> > boundary. I find using one logically selected residue or atom is the 
> > best method here.
> >
> > 6. Assuming that you got what you wanted in step 5, now run g_traj and 
> > g_dist on final_center.gro. In my case, I found that g_traj and g_dist 
> > give the same answer as the pull code output when I am using 
> > final_center.gro, but not always when I am using final.gro.
> >
> > *** I always laugh when these problems arise because, in an important 
> > sense, the protein *did* jump out of the simulation box... at least as 
> > far as g_traj and g_dist are concerned. This, we must hope, is 
> > correctly treated in the pull code even though it is incorrectly (or 
> > at least unintuitively) treated by g_traj and g_dist.
> >
> > Chris.
> >
> > -- original message --
> >
> > Hi,
> >
> > Thank you Berk and Chris for the suggestions.
> >
> > To address the possibility that this issue is related to periodic
> > boundaries, I used two approaches:
> > 1.  The pull group of interest (permeant) was centered in the x-y plane
> > of the box using Chris' approach.  I then used the genconf utility to
> > replicate my lipid box to a 9x9 grid in the x-y plane and removed all
> > but the center box.  This generated the coordi

[gmx-users] ligand-protein distance restraint

[Pathumwadee Intharathep]

Dear gmx-user,
 
I put #include "disre.itp"   at the end of making a hybrid [molecule] section 
as mark's suggestion, I got the same error after grompp. 

  
“Fatal error: [ file "../disre.itp", line 2 ]: 
 Atom index (195) in distance_restraints out of bounds (1-1)” 
 
;   File 'top.top' was generated; Include forcefield parameters
;
#include "/home/bio001/02_saow/gromacs_top/jit/top/ffgmx.itp"
#include "/home/bio001/02_saow/gromacs_top/jit/popc.itp"
; Include chain topologies
#include "1add_H/0H_addH1.top"  ;protein atom 1-1615
#include "rimq1_top.itp"  ;ligand topology file 1-16
; Include water topology
#include "/home/bio001/02_saow/gromacs_top/jit/top/flexspc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcx    fcy    fcz
   1    1   1000   1000   1000
#endif
; Include generic topology for ions
#include "/home/bio001/02_saow/gromacs_top/jit/top/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound    #mols
Protein_A 1
RIM      4
POPC  74
SOL   3763
Cl       8
#include "disre.itp"   
-- 
detailed in "disre.itp" file is
[ distance_restraints ] 
 195   1628   1   1 1   0.25 0.35 0.40 1.0 
     195    563   1   1 1   0.25 0.35 0.40 1.0 
     598   1644   1   1 1   0.25 0.35 0.40 1.0 
     598    966   1   1 1   0.25 0.35 0.40 1.0 
    1001   1660   1   1 1   0.25 0.35 0.40 1.0 
    1001    369   1   1 1   0.25 0.35 0.40 1.0 
    1404   1676   1   1 1   0.25 0.35 0.40 1.0 
    1404    160   1   1 1   0.25 0.35 0.40 1.0 

I also try to merge the ligand into protein topology by using pdb2gmx but it 
can not file the forcefield for ligand. 
  

 Thanks so much
 
pathum



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[gmx-users] Software inconsistency error.

[Homa Azizian]

Hi
I want to have cg minimization after steep minimization of my MD result .
but every time this error appeare. 

<>

What could be the reason ?
Thanks.




--
Tehran University of Medical Sciences
www.tums.ac.ir


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Re: [gmx-users] ligand-protein distance restraint

[Mark Abraham]

Pathumwadee Intharathep wrote:

Dear Mark,
 
I put #include "disre.itp"   at the end of making a hybrid [molecule] 
section as you've suggested, I got the same error after grompp. 


No, you didn't put it at the end of a [moleculetype] section. These must 
all start and finish before the [system] directive. See manual section 5.7


Apologies for specifying [molecule] earlier - obviously I meant 
[moleculetype].


Mark
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