[gmx-users] About entropic contribution to the potential of mean force

[Zhang Zhigang]

Hi,
In the manual of gromacs, the entropic contribution to the pmf is
emphasized. In my opinion, this contribution is originated from the
rotations of the constrained groups.
However, according to the manual suggestion, ...when calculating a PMF
between two solutes in a solvent, for the purpose of simulating without
solvent, the entropic contribution should be removed. I'm really confused
with this.
If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl-
and many water molecules), I want to calculate the potential of mean force
of NaCl, should I count the contributions from the entropic effects?
According to Hess et al., (2006), JCP, 124: 164509, this effect should
surely be added.
So, any one experienced with similar researches can give me an answer
for this: when should I add the entropic contribution to the pmfs? and, what
the really physical explanation for this effect?
Thanks in advance!

Regards,

zgzhang
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Re: [gmx-users] Using double precision files with single precision version

[Mark Abraham]

vivek sharma wrote:

Hi All,
I had a few MD runs with double precision in gromacs, Can I use single 
precision version of gromacs to play with those files e.g making movie 
files and extracting h_bond information.

I am afraid if it will affect my results.


I don't know whether it does work, but I suspect not. However it's 
trivial to compile a double-precision version, with --enable-double and 
--program-suffix=_d, and once installed you can use g_hbond when you 
want and g_hbond_d when you want.


Mark
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Re: [gmx-users] Replacing molecules in .gro coordinate file

[Omer Markovitch]

 Supposed I have a .gro file of 38 molecules of A which are already in
 equilibrated conformations. Now I want to transform 15 molecules of A into B
 therefore I will have the binary mixture of A/B with 13:15 molar ratio in
 the final structure. How can I do this? Any suggestions will be appreciated.


Maybe open A  B in vmd together, and then save them as one PDB? Omer.
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Re: [gmx-users] Analyzing a trajectory split over multiple files

[Omer Markovitch]

On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty
[EMAIL PROTECTED]wrote:

 Dear all,

 I have a very long trajectory split over a large number of files. What
 would be the most efficient way to use the analysis programs over them?
 Do they support multiple input for trajectory? Or I need to combine all
 files into a single one anyway?


You should analyze each individual part on its own, and output the raw data
of the result, then average the parts together.

For example - say you are interested in coordination number of molecule X:
For each part, output both the total number of X's found, plus the total
number of X neighbors found. The coordination number is then the sum of
neig. divided by the sum of X's, from ALL parts.
It might be an issue if each part has different time length, then averaging
the coordination number of each part might give more statistical weigh to
short parts then they should have.

In other words, you should first collect the data of each part together, and
only then avg..

--Omer.
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Re: [gmx-users] Re: how to show dodecahedron box in VMD

[Tsjerk Wassenaar]

Hi,

Can't help you with VMD, but I do have a script to take care of this in Pymol.

Cheers,

Tsjerk

On 11/25/08, xianghong qi [EMAIL PROTECTED] wrote:
 Dear all:

 I am trying to show the dodecahedron box only in vmd since my simulation box
 is dodecahedron.  If I include water, I can see the box is dodecahedron. But
 I want to get rid off all of water, then my box will not appear there. How
 can I keep the dodecahedron box boundaries and solute only? Looks like only
 the rectangular box boundaries can be drawn  in VMD.
  Does anyone has some suggestions? Appreciate your great help.
 Happy Thanksgiving.
 -Xianghong Qi

 --
 Some people make the world more special just by being in it.

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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] List of all bonds form tpr file?

[Berk Hess]

Hi,

gmxdump in 4.0 still dumps all bonds.
I don't know what causes you not to see them.

Berk

 Date: Wed, 26 Nov 2008 02:09:08 -0800
 From: [EMAIL PROTECTED]
 To: gmx-users@gromacs.org
 Subject: [gmx-users] List of all bonds form tpr file?
 
 Dear All,
 We have a script, which visualizes the bonds in the coarse-grained system 
 simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files 
 and extracted BONDS records. Now in 4.x it does not work because gmxdump no 
 longer outputs all bonds in the system. Is it possible to extract information 
 about *all* bonds in the system (not only the bonds in each moleculetype) 
 from tpr file in 4.x?
 
 Any help is appreciated!
 
 Semen
 
 
 
 
 - Original Message 
 From: Mark Abraham [EMAIL PROTECTED]
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Sent: Wednesday, November 19, 2008 1:57:19 PM
 Subject: Re: [gmx-users] Pulling in 4.0  - Any documentation?
 
 Semen Esilevsky wrote:
  Dear All,
  Where can I find documentation about the pull code in Gromacs 4.0? As far 
  as I understand old style of setting up pulling simulations in separate 
  file does not work any more, but I can't figure out how to transfer pulling 
  params correctly to mdp file. Any help is appreciated!
  
  P.S. Probably the developers could put at least some very brief docs on web 
  site while new manual is being prepared? Otherwise new cool features of 4.0 
  just can't be used by ordinary users...
 
 The beta manual is at ftp://ftp.gromacs.org/pub/beta/
 
 Mark
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RE: [gmx-users] List of all bonds form tpr file?

[Berk Hess]

I just realized that in 4.0 I modified things such that it only
prints the bonds per molecule type.
It would be quite easy to modify a program to write all bonds.
(mk_angdx for instance).

If you just have one atom type you can easily modify
your script by reading the number of molecules and atoms_mol
from the molblock print in the gmxdump output.

Berk

From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] List of all bonds form tpr file?
Date: Wed, 26 Nov 2008 11:52:45 +0100








Hi,

gmxdump in 4.0 still dumps all bonds.
I don't know what causes you not to see them.

Berk

 Date: Wed, 26 Nov 2008 02:09:08 -0800
 From: [EMAIL PROTECTED]
 To: gmx-users@gromacs.org
 Subject: [gmx-users] List of all bonds form tpr file?
 
 Dear All,
 We have a script, which visualizes the bonds in the coarse-grained system 
 simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files 
 and extracted BONDS records. Now in 4.x it does not work because gmxdump no 
 longer outputs all bonds in the system. Is it possible to extract information 
 about *all* bonds in the system (not only the bonds in each moleculetype) 
 from tpr file in 4.x?
 
 Any help is appreciated!
 
 Semen
 
 
 
 
 - Original Message 
 From: Mark Abraham [EMAIL PROTECTED]
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Sent: Wednesday, November 19, 2008 1:57:19 PM
 Subject: Re: [gmx-users] Pulling in 4.0  - Any documentation?
 
 Semen Esilevsky wrote:
  Dear All,
  Where can I find documentation about the pull code in Gromacs 4.0? As far 
  as I understand old style of setting up pulling simulations in separate 
  file does not work any more, but I can't figure out how to transfer pulling 
  params correctly to mdp file. Any help is appreciated!
  
  P.S. Probably the developers could put at least some very brief docs on web 
  site while new manual is being prepared? Otherwise new cool features of 4.0 
  just can't be used by ordinary users...
 
 The beta manual is at ftp://ftp.gromacs.org/pub/beta/
 
 Mark
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Re: [gmx-users] Re: how to show dodecahedron box in VMD

[Alessandro Casoni]

Tsjerk Wassenaar ha scritto:

Hi,

Can't help you with VMD, but I do have a script to take care of this in Pymol.

Cheers,

Tsjerk

On 11/25/08, xianghong qi [EMAIL PROTECTED] wrote:
  

Dear all:

I am trying to show the dodecahedron box only in vmd since my simulation box
is dodecahedron.  If I include water, I can see the box is dodecahedron. But
I want to get rid off all of water, then my box will not appear there. How
can I keep the dodecahedron box boundaries and solute only? Looks like only
the rectangular box boundaries can be drawn  in VMD.
 Does anyone has some suggestions? Appreciate your great help.
Happy Thanksgiving.
-Xianghong Qi

--
Some people make the world more special just by being in it.

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Hi,
you can try this:

trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact*

or

trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1

well...the first converts all your trajectory and the last command 
extracts 1 frame in a gro file..


good luck
alessandro


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Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

[Justin A. Lemkul]

Justin A. Lemkul wrote:

S and Fe atoms to be 0.25 +/- 0.2 nm apart.  If they are much further 


Edit that: 0.25 nm +/- 0.02 nm.  Apparently my math (and/or typing) skills are 
suspect first thing in the morning :)


-Justin

--


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


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Re: [gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

[Daniel Seeliger]

Hi, 
I also encoutered a strange behaviour of gmxcpp when using B-states.

When I set up up a free energy simulation (gromacs 4.0.2) with amber03 
(ffamber from Sorin  Pande), I define a dihedral angle, e.g. like

[ dihedrals ]
.
511  515  517  513 3 aromatic_prop_5aaromatic_prop_5
.
If I process this topology with grompp it claims that there is no B-state 
defined.

In the original ffamber03bon.itp there were comments in the define lines, e.g.

#define  aromatic_prop_5  41.84000 0.0   -41.84000 0.0 
0.0 0.0 ;  X-CR-NB-X (HIX)

These were already removed since this causes grompp to cut the line after the 
first ; and, hence it ignores the B-values.

Now the strange thing:
This works for all defined dihedrals except for those that end with an a.
So:
12 3 4  aromatic_prop_4  aromatic_prop_5
works fine, but
12 3 4  aromatic_prop_5a  aromatic_prop_5
doesn't work. 
 
If I look into the processed topology, grompp has converted the first define, 
but not the second one.
If I exchange the two dihedrals, like
12 3 4  aromatic_prop_5  aromatic_prop_5a
it works again.

I get the error only when these dihedrals are in the A-state:
aromatic_prop_4a
aromatic_prop_5a
aromatic_prop_6a

If I preprocess my topology with cpp -traditional all defines are nicely 
converted, so I guess there must go sth. wrong in gmxcpp.
I also tried the fixed version from Berk as pointed out before, but this 
didn't do the job.

Thanks,
Daniel

On Tuesday 25 November 2008 23:34:24 Berk Hess wrote:
 Hi,

 That  is an annoying bug.
 I fixed it for 4.0.3.
 If you want it fixed now, the diff is below.

 Berk


 RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v
 retrieving revision 1.9
 diff -r1.9 gmxcpp.c
 121,122c121,122
sscanf(define,%s,name);
ptr = define + strlen(name);
 ---

sscanf(define,%s%n,name,i);
ptr = define + i;
 
 
  Date: Tue, 25 Nov 2008 16:32:57 -0500
  From: [EMAIL PROTECTED]
  To: gmx-users@gromacs.org
  Subject: [gmx-users] correct processing of #define statements by grompp
  in gromacs 4.0.2 requires exactly one space after #define
 
  When two spaces are included the #define KEYWORD is incompletely removed
  from the file.
  In case my conclusion about the exact nature of the error is incorrect,
  here is more information.
 
  I have a ffcharmbon.itp file that contains:
 
  [ dihedraltypes ]
  #define  improper_NC2_X_X_C_  180.0  83.68000  2
 
  And an .itp file that contains:
 
  [ dihedrals ]
  1 2 5 8 1 improper_NC2_X_X_C_
 
  where grompp -pp returns
 
  [ dihedrals ]
  1 2 5 8 1 _  180.0  83.68000  2
 
  and the floating '_' character causes the error message:
 
  ERROR 1 [file my.itp, line 77]:
No default Proper Dih. types
 
  I tried to fix this by removing the trailing underscore character from
  my defined string in both files,
  but now I get a trailing 'C'
 
  [ dihedrals ]
  1 2 5 8 1 C  180.0  83.68000  2
 
  So it appears that the define statement is simply not being entirely
  removed.
 
  When I then replaced
  #define  improper_NC2_X_X_C_  180.0  83.68000  2
  by
  #define improper_NC2_X_X_C_  180.0  83.68000  2
  (only one space between '#define' and 'improper...')
  it works correctly.
 
  Note that cpp handled this original define statement properly in gromacs
  3.3.1.
 
  Chris.
 
 
 
 
 
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-- 
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Computational Biomolecular Dynamics Group
Max-Planck-Institute for Biophysical Chemistry  
Am Fassberg 11
37077 Goettingen, Germany
Tel: +49 551 201 2310
Fax: +49 551 201 2302
email: [EMAIL PROTECTED]
www.mpibpc.mpg.de/groups/de_groot/dseelig/index.html
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[gmx-users] Problems with distance restraints

[Justin A. Lemkul]

Hi all,

I am trying to use a simple scheme to restrain a few distances within my 
protein, which is contained within an octahedral box of SPC water.


In place of distance restraints, I'm using bond type 6 to utilize a harmonic 
potential to restrain the distance between a few atoms.  When I imposed one such 
restraint in the topology, the simulation ran fine.  After finishing this 
trajectory, I wanted to impose a second restraint and try again.  At this point, 
the simulation fails with the following:


mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt

snip

Initializing Domain Decomposition on 24 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 1.634 nm
  multi-body bonded interactions: 0.606 nm
Minimum cell size due to bonded interactions: 1.797 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm
Estimated maximum distance required for P-LINCS: 0.876 nm
Guess for relative PME load: 0.45
Will use 12 particle-particle and 12 PME only nodes
This is a guess, check the performance at the end of the log file
Using 12 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm
The maximum allowed number of cells is: X 2 Y 2 Z 2

---
Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2
Source code file: domdec.c, line: 5842

Fatal error:
There is no domain decomposition for 12 nodes that is compatible with the given 
box and a minimum cell size of 2.24633 nm

Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
---

I'm Only Faking When I Get It Right (Soundgarden)

I realize there are more optimizations I could impose to better balance the 
PP/PME load.  I have tried those (altering my cutoff's and grid spacing) but it 
makes no difference.  Plus, I'd like to remain consistent with the original 
simulation that used only one restraint.  If I remove the second restraint, the 
simulation runs just fine.  For reference, the restraints I'm imposing are:


  330  1016 60.669   5.0300e+06
 1016   559 60.376   5.0300e+06

The box vectors from the .gro file are:

   7.14132   6.73290   5.83086   0.0   0.0   2.38044   0.0 
-2.38044   3.36645


Is there anything obvious that I'm doing wrong?  Or should I just use real 
distance restraints, according to manual section 4.3.4?  Thanks for any insights.


-Justin

--


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


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Re: [gmx-users] Problems with distance restraints

[Justin A. Lemkul]

Please disregard my message.  I had a typo in my atom numbers that I was 
restraining.  Apparently the distance between atoms 1016 and 559 is far greater 
than 0.376 nm, thus generating the error.


-Justin

Justin A. Lemkul wrote:


Hi all,

I am trying to use a simple scheme to restrain a few distances within my 
protein, which is contained within an octahedral box of SPC water.


In place of distance restraints, I'm using bond type 6 to utilize a 
harmonic potential to restrain the distance between a few atoms.  When I 
imposed one such restraint in the topology, the simulation ran fine.  
After finishing this trajectory, I wanted to impose a second restraint 
and try again.  At this point, the simulation fails with the following:


mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt

snip

Initializing Domain Decomposition on 24 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 1.634 nm
  multi-body bonded interactions: 0.606 nm
Minimum cell size due to bonded interactions: 1.797 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm
Estimated maximum distance required for P-LINCS: 0.876 nm
Guess for relative PME load: 0.45
Will use 12 particle-particle and 12 PME only nodes
This is a guess, check the performance at the end of the log file
Using 12 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm
The maximum allowed number of cells is: X 2 Y 2 Z 2

---
Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2
Source code file: domdec.c, line: 5842

Fatal error:
There is no domain decomposition for 12 nodes that is compatible with 
the given box and a minimum cell size of 2.24633 nm

Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
---

I'm Only Faking When I Get It Right (Soundgarden)

I realize there are more optimizations I could impose to better balance 
the PP/PME load.  I have tried those (altering my cutoff's and grid 
spacing) but it makes no difference.  Plus, I'd like to remain 
consistent with the original simulation that used only one restraint.  
If I remove the second restraint, the simulation runs just fine.  For 
reference, the restraints I'm imposing are:


  330  1016 60.669   5.0300e+06
 1016   559 60.376   5.0300e+06

The box vectors from the .gro file are:

   7.14132   6.73290   5.83086   0.0   0.0   2.38044   0.0 
-2.38044   3.36645


Is there anything obvious that I'm doing wrong?  Or should I just use 
real distance restraints, according to manual section 4.3.4?  Thanks for 
any insights.


-Justin



--


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


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[gmx-users] gmx-users@gromacs.org

[H.J.Risselada]

Finally had a look through the gromacs 4.0 source code.
Don't know if this bug/points already have been reported and changed 
in 4.0.2:


1) There is never memory allocated for the pointers to the user 
defined groups:


mdatoms-cU1 etc.

These pointers will stay NULL when a user defined group is defined in 
the mdp file.
I find these groups normally a pretty useful interface for simple fast 
implementations.


2) The pull code has indeed completely changed, however to me the 
questionable factor 0.5 remained the same:

  In pull.c:

/* Add the pull contribution to the virial */
 vir[j][m] += 0.5*f[j]*r_ij[g][m];

I do agree with the positive sign of the summation,  but why is there 
a factor 0.5 to correct for double counting included in the summation. 
The summation is already ordered as r_ij and f[j] is the distance 
vector and force between the particle and the equilibrium position of 
the spring and therefore double counting cannot occur.  Ofcourse it's 
possible that this factor 0.5 is not meant as a double counting 
correction factor, but then I don't see where it does come from. If 
this factor is indeed incorrect it might affect the pressure 
significantly in case a large pulling group is used.


greetings

Jelger
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[gmx-users] Bugs in gromacs 4

[Jelger Risselada]

Finally had a look through the gromacs 4.0 source code.
Don't know if this bug/points already have been reported and changed in 
4.0.2:


1) There is never memory allocated for the pointers to the user defined 
groups:


mdatoms-cU1 etc.

These pointers will stay NULL when a user defined group is defined in 
the mdp file.
I find these groups normally a pretty useful interface for simple fast 
implementations.


2) The pull code has indeed completely changed, however to me the 
questionable factor 0.5 remained the same:

  In pull.c:

/* Add the pull contribution to the virial */
 vir[j][m] += 0.5*f[j]*r_ij[g][m];

I do agree with the positive sign of the summation,  but why is there a 
factor 0.5 to correct for double counting included in the summation. The 
summation is already ordered as r_ij and f[j] is the distance vector and 
force between the particle and the equilibrium position of the spring 
and therefore double counting cannot occur.  Ofcourse it's possible that 
this factor 0.5 is not meant as a double counting correction factor, but 
then I don't see where it does come from. If this factor is indeed 
incorrect it might affect the pressure significantly in case a large 
pulling group is used.


greetings

Jelger

























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Re: [gmx-users] Re: how to show dodecahedron box in VMD

[xianghong qi]

Thanks lot. Happy Thanksgiving!.
-Xianghong Qi

On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni 
[EMAIL PROTECTED] wrote:

 Tsjerk Wassenaar ha scritto:

 Hi,

 Can't help you with VMD, but I do have a script to take care of this in
 Pymol.

 Cheers,

 Tsjerk

 On 11/25/08, xianghong qi [EMAIL PROTECTED] wrote:


 Dear all:

 I am trying to show the dodecahedron box only in vmd since my simulation
 box
 is dodecahedron.  If I include water, I can see the box is dodecahedron.
 But
 I want to get rid off all of water, then my box will not appear there.
 How
 can I keep the dodecahedron box boundaries and solute only? Looks like
 only
 the rectangular box boundaries can be drawn  in VMD.
  Does anyone has some suggestions? Appreciate your great help.
 Happy Thanksgiving.
 -Xianghong Qi

 --
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 Hi,
 you can try this:

 trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact*

 or

 trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1

 well...the first converts all your trajectory and the last command extracts
 1 frame in a gro file..

 good luck
 alessandro



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[gmx-users] List of all bonds form tpr file?

[Semen Esilevsky]

Dear All,
We have a script, which visualizes the bonds in the coarse-grained system 
simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files and 
extracted BONDS records. Now in 4.x it does not work because gmxdump no longer 
outputs all bonds in the system. Is it possible to extract information about 
*all* bonds in the system (not only the bonds in each moleculetype) from tpr 
file in 4.x?

Any help is appreciated!

Semen




- Original Message 
From: Mark Abraham [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wednesday, November 19, 2008 1:57:19 PM
Subject: Re: [gmx-users] Pulling in 4.0  - Any documentation?

Semen Esilevsky wrote:
 Dear All,
 Where can I find documentation about the pull code in Gromacs 4.0? As far as 
 I understand old style of setting up pulling simulations in separate file 
 does not work any more, but I can't figure out how to transfer pulling params 
 correctly to mdp file. Any help is appreciated!
 
 P.S. Probably the developers could put at least some very brief docs on web 
 site while new manual is being prepared? Otherwise new cool features of 4.0 
 just can't be used by ordinary users...

The beta manual is at ftp://ftp.gromacs.org/pub/beta/

Mark
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Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:

Hi Justin,
Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said
the topology file does contain the bonds and I need not have made the
modificatins to specbond.dat. But using the original specbond.dat does not
prevent the protonation of CYS. I renamed CYS as CYS2 in the input pdb
file and used the following command line
pdb2gmx_mpi -ignh -ff gmx -f 2c9_s50.pdb -o protein_h.pdb -p  
topology.top -water spce

Am I  missing some crucial option here (like -ss for disulphide bonds)?
Thanks once again.


One piece of general advice - don't use ffgmx.  It has long been deprecated 
(according to the manual, the output of pdb2gmx, and dozens of posts on this 
list).  Use one of the newer Gromos96 force fields.


Now, to address the actual question :)  The only thing I can think of is that 
specbond.dat uses a simple distance search to determine if the atoms are bonded, 
and I believe the tolerance is something like 10%.  So the value in specbond.dat 
of 0.25 implies that pdb2gmx should expect the S and Fe atoms to be 0.25 +/- 0.2 
nm apart.  If they are much further apart, no bond will be detected.  Check your 
input .pdb file to see how far apart these two atoms are.


-Justin


Regards,
Sarada



Message: 6
Date: Tue, 25 Nov 2008 07:17:14 -0500
From: Justin A. Lemkul [EMAIL PROTECTED]
Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=UTF-8; format=flowed



[EMAIL PROTECTED] wrote:

Hello,
Sorry, I realised the HEME HEC naming was not the problem. But still the
pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
protonated and doesnot form a bond with HEME. I tried to preserve the
bonds by editing the specbond.dat file. I do not know if it can be used
for intramolecular bonding. Kindly inform if the modifications I have
made
are valid. The runtime information during the execution of pdb2gmx
indicated the linking of FE in HEME to the N atoms. However, I do not
see
the bonds when I open the output file in Pymol. Please indicate how this
problem can be resolved.


Well, using visualization software may not indicate anything.  Most
programs
decide on bonds based on distance, not any sort of intelligent mechanism.
The
question is whether or not these bonds show up in your topol.top.


This is the content of my specbond.dat file:

5
CYS SG  1   HEMEFE  5   0.25CYS HEME

Well, this may be why your Cys is getting protonated - you're telling
pdb2gmx
that it should be!  See the format of specbond.dat here:

http://wiki.gromacs.org/index.php/specbond.dat

The second-to-last column should be the new residue name for cysteine,
probably
you want something like CYS2.


HEMEFE  5   HEMENA  3   0.22HEMEHEME
HEMEFE  5   HEMENB  3   0.22HEMEHEME
HEMEFE  5   HEMENC  3   0.22HEMEHEME
HEMEFE  5   HEMEND  3   0.22HEMEHEME


Why is this section (above) even necessary?  Are these bonds not defined
in the
.rtp file of your force field?  Which force field are you using?  I know
these
are defined in the Gromos-type force fields.

Try again with the original specbond.dat, but don't assume that
visualization
software will always indicate the presence/absence of a bond.  Examine
your
topology for that.

-Justin


And these I obtained during the execution of pdbgmx:

Opening library file specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
  CYS122  CYS135  CYS143  CYS146  CYS150  CYS237  CYS309
   SG958  SG1059  SG1118  SG1136  SG1165  SG1902  SG2475
  CYS135  SG1059   1.677
  CYS143  SG1118   1.076   1.092
  CYS146  SG1136   1.313   1.792   0.749
  CYS150  SG1165   1.175   2.054   0.978   0.426
  CYS237  SG1902   2.194   3.510   2.536   1.933   1.632
  CYS309  SG2475   1.745   2.703   2.469   2.507   2.423   2.449
  CYS343  SG2748   4.679   4.998   4.364   3.763   3.870   3.329   4.426
  CYS406  SG3265   2.258   2.657   2.051   1.603   1.744   1.886   2.198
  CYS457  SG3657   2.232   0.829   1.894   2.582   2.825   4.173   2.898
 HEME462  FE3693   2.257   2.566   1.949   1.489   1.669   1.956   2.343
 HEME462  NA3694   2.456   2.680   2.110   1.663   1.862   2.118   2.486
 HEME462  NB3695   2.199   2.426   1.883   1.498   1.704   2.088   2.247
 HEME462  NC3696   2.061   2.462   1.795   1.321   1.479   1.809   2.217
 HEME462  ND3697   2.331   2.711   2.031   1.505   1.657   1.841   2.455
  CYS343  CYS406  CYS457 HEME462 HEME462 HEME462 HEME462
  SG2748  SG3265  SG3657  FE3693  NA3694  NB3695  NC3696
  CYS406  SG3265   2.501
  CYS457  SG3657   5.547   3.210
 HEME462  FE3693   2.512   0.219   3.147
 HEME462  NA3694   2.361   0.325   3.240   0.211
 HEME462  NB3695   

RE: [gmx-users] Using double precision files with single precision version

[Berk Hess]

Hi,

This works fine.
All Gromacs file format/programs are single/double compatible both ways.
Reading a double precision file with a single precision program,
or course, gives single precision results.
But there is probably no property that is significantly affected by this.

Berk

 Date: Wed, 26 Nov 2008 20:14:28 +1100
 From: [EMAIL PROTECTED]
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] Using double precision files with single precision   
 version
 
 vivek sharma wrote:
  Hi All,
  I had a few MD runs with double precision in gromacs, Can I use single 
  precision version of gromacs to play with those files e.g making movie 
  files and extracting h_bond information.
  I am afraid if it will affect my results.
 
 I don't know whether it does work, but I suspect not. However it's 
 trivial to compile a double-precision version, with --enable-double and 
 --program-suffix=_d, and once installed you can use g_hbond when you 
 want and g_hbond_d when you want.
 
 Mark
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Re: [gmx-users] Bugs in gromacs 4

[Jochen Hub]

Jelger Risselada wrote:
 Finally had a look through the gromacs 4.0 source code.
 Don't know if this bug/points already have been reported and changed in
 4.0.2:
 
 1) There is never memory allocated for the pointers to the user defined
 groups:
 
 mdatoms-cU1 etc.

I'm not sure, but there is a

/* The user should fix this */
if (FALSE)
  srenew(md-cU1,md-nalloc);
if (FALSE)
  srenew(md-cU2,md-nalloc);

in ./src/mdlib/mdatom.c.

You can remove the FALSE and get the memory allocation, I guess.

Jochen

 
 These pointers will stay NULL when a user defined group is defined in
 the mdp file.
 I find these groups normally a pretty useful interface for simple fast
 implementations.
 
 2) The pull code has indeed completely changed, however to me the
 questionable factor 0.5 remained the same:
   In pull.c:
 
 /* Add the pull contribution to the virial */
  vir[j][m] += 0.5*f[j]*r_ij[g][m];
 
 I do agree with the positive sign of the summation,  but why is there a
 factor 0.5 to correct for double counting included in the summation. The
 summation is already ordered as r_ij and f[j] is the distance vector and
 force between the particle and the equilibrium position of the spring
 and therefore double counting cannot occur.  Ofcourse it's possible that
 this factor 0.5 is not meant as a double counting correction factor, but
 then I don't see where it does come from. If this factor is indeed
 incorrect it might affect the pressure significantly in case a large
 pulling group is used.
 
 greetings
 
 Jelger
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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 .
 


-- 

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

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[gmx-users] Problems with distance restraints

[chris . neale]

It's not really a solution, but you could try a different number of  
nodes. I have found that even regular topologies might run on N nodes,  
but not N+A nodes, giving the error messaeg that you post below.


Chris.

-- original message --

Hi all,

I am trying to use a simple scheme to restrain a few distances within my
protein, which is contained within an octahedral box of SPC water.

In place of distance restraints, I'm using bond type 6 to utilize a harmonic
potential to restrain the distance between a few atoms.  When I  
imposed one such

restraint in the topology, the simulation ran fine.  After finishing this
trajectory, I wanted to impose a second restraint and try again.  At  
this point,

the simulation fails with the following:

mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt

snip

Initializing Domain Decomposition on 24 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
 two-body bonded interactions: 1.634 nm
   multi-body bonded interactions: 0.606 nm
Minimum cell size due to bonded interactions: 1.797 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm
Estimated maximum distance required for P-LINCS: 0.876 nm
Guess for relative PME load: 0.45
Will use 12 particle-particle and 12 PME only nodes
This is a guess, check the performance at the end of the log file
Using 12 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm
The maximum allowed number of cells is: X 2 Y 2 Z 2

---
Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2
Source code file: domdec.c, line: 5842

Fatal error:
There is no domain decomposition for 12 nodes that is compatible with  
the given

box and a minimum cell size of 2.24633 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
---

I'm Only Faking When I Get It Right (Soundgarden)

I realize there are more optimizations I could impose to better balance the
PP/PME load.  I have tried those (altering my cutoff's and grid  
spacing) but it

makes no difference.  Plus, I'd like to remain consistent with the original
simulation that used only one restraint.  If I remove the second  
restraint, the

simulation runs just fine.  For reference, the restraints I'm imposing are:

   330  1016 60.669   5.0300e+06
  1016   559 60.376   5.0300e+06

The box vectors from the .gro file are:

7.14132   6.73290   5.83086   0.0   0.0   2.38044   0.0
-2.38044   3.36645

Is there anything obvious that I'm doing wrong?  Or should I just use real
distance restraints, according to manual section 4.3.4?  Thanks for  
any insights.


-Justin

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RE: [gmx-users] course grain model for DNA

[He, Yang]

Hi Justin,

Thank you for your reply. In fact , for this base pair of Gb2  Cb2  1  
0.000194e10   0.00217e4,  whatever I do , the final result for this base pair 
is the same they will always separate from each other. Hence, I doubt whether 
this is because gromacs did not read my force field file at all.

I hope to get your further suggestions about that.

Thank you .

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Tuesday, November 25, 2008 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] course grain model for DNA

He, Yang wrote:
 Hi all users,

 when I am using the gromacs to simulate the course grain model for DNA, it 
 seems that the software doesn't recognize my force field file. I have 
 included all the bond and non-bond parameters in the bon.itp and nb.itp file.

 During my simulation , I found that the base pair for C-G which first are in 
 the balance distance always repel from each other so I try to increase the 
 value of epsilon to increase the dispersion between this pair but it still 
 did not work and the pair still  repelled  from each other after the 
 simulation .

 Then I tried like this;  Gb2  Cb2  1  0.000194e10   0.00217e4  
 in my nb.itp file,  I found that the simulation can still be carried on and 
 the simulation result is the same for this base pair.


Well, that line is commented out (;), so naturally it would have no effect.

-Justin

 So ,I got confused about this phenomenon . Can anyone of you give me some 
 suggestions?

 Thank you in advance.

 Yang
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--


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


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RE: [gmx-users] course grain model for DNA

[He, Yang]

Hi Mrinalini.

Thank you for your suggestions. In my previous case, I never use the distance 
restraints . So I wonder whether you can provide me a sample for file of the 
disres.itp .In fact, I don't know much about this file' form and how to set 
values in the file.

Thank you.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mrinalini Puranik [EMAIL 
PROTECTED]
Sent: Tuesday, November 25, 2008 3:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] course grain model for DNA

If there is fraying at the edges only, you can impose distance
restraints on some of the hydrogen bonds at the ends. You need to
modify md.mdp to turn on distance restraints and have a new file
called disres.itp that mentions the distances to be restrained.

Hope this helps,
Mrinalini


On Wed, Nov 26, 2008 at 1:06 AM, He, Yang [EMAIL PROTECTED] wrote:
 Hi all users,

 when I am using the gromacs to simulate the course grain model for DNA, it 
 seems that the software doesn't recognize my force field file. I have 
 included all the bond and non-bond parameters in the bon.itp and nb.itp file.

 During my simulation , I found that the base pair for C-G which first are in 
 the balance distance always repel from each other so I try to increase the 
 value of epsilon to increase the dispersion between this pair but it still 
 did not work and the pair still  repelled  from each other after the 
 simulation .

 Then I tried like this;  Gb2  Cb2  1  0.000194e10   0.00217e4  
 in my nb.itp file,  I found that the simulation can still be carried on and 
 the simulation result is the same for this base pair.

 So ,I got confused about this phenomenon . Can anyone of you give me some 
 suggestions?

 Thank you in advance.

 Yang
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Re: [gmx-users] course grain model for DNA

[Justin A. Lemkul]

He, Yang wrote:

Hi Mrinalini.

Thank you for your suggestions. In my previous case, I never use the distance 
restraints . So I wonder whether you can provide me a sample for file of the 
disres.itp .In fact, I don't know much about this file' form and how to set 
values in the file.



Manual section 4.3.4; it doesn't have to be a separate .itp file if you don't 
want.  You can just add a [ distance_restraints ] section in your system topology.


-Justin


Thank you.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mrinalini Puranik [EMAIL 
PROTECTED]
Sent: Tuesday, November 25, 2008 3:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] course grain model for DNA

If there is fraying at the edges only, you can impose distance
restraints on some of the hydrogen bonds at the ends. You need to
modify md.mdp to turn on distance restraints and have a new file
called disres.itp that mentions the distances to be restrained.

Hope this helps,
Mrinalini


On Wed, Nov 26, 2008 at 1:06 AM, He, Yang [EMAIL PROTECTED] wrote:

Hi all users,

when I am using the gromacs to simulate the course grain model for DNA, it 
seems that the software doesn't recognize my force field file. I have included 
all the bond and non-bond parameters in the bon.itp and nb.itp file.

During my simulation , I found that the base pair for C-G which first are in 
the balance distance always repel from each other so I try to increase the 
value of epsilon to increase the dispersion between this pair but it still did 
not work and the pair still  repelled  from each other after the simulation .

Then I tried like this;  Gb2  Cb2  1  0.000194e10   0.00217e4  in 
my nb.itp file,  I found that the simulation can still be carried on and the simulation 
result is the same for this base pair.

So ,I got confused about this phenomenon . Can anyone of you give me some 
suggestions?

Thank you in advance.

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


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Re: [gmx-users] course grain model for DNA

[Justin A. Lemkul]

He, Yang wrote:

Hi Justin,

Thank you for your reply. In fact , for this base pair of Gb2  Cb2  1  
0.000194e10   0.00217e4,  whatever I do , the final result for this base pair is 
the same they will always separate from each other. Hence, I doubt whether this is 
because gromacs did not read my force field file at all.

I hope to get your further suggestions about that.



What magnitude of values have you tried?  Using 0.000194e10 (1.94e7) for epsilon 
seems huge, but then, the only CG force field I've ever used is MARTINI (and 
only with only a little experience).  The magnitudes of sigma and epsilon for 
that force field are on the order of e0, e-01, etc.


How are you determining your sigma and epsilon values?

-Justin


Thank you .

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Tuesday, November 25, 2008 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] course grain model for DNA

He, Yang wrote:

Hi all users,

when I am using the gromacs to simulate the course grain model for DNA, it 
seems that the software doesn't recognize my force field file. I have included 
all the bond and non-bond parameters in the bon.itp and nb.itp file.

During my simulation , I found that the base pair for C-G which first are in 
the balance distance always repel from each other so I try to increase the 
value of epsilon to increase the dispersion between this pair but it still did 
not work and the pair still  repelled  from each other after the simulation .

Then I tried like this;  Gb2  Cb2  1  0.000194e10   0.00217e4  in 
my nb.itp file,  I found that the simulation can still be carried on and the simulation 
result is the same for this base pair.



Well, that line is commented out (;), so naturally it would have no effect.

-Justin


So ,I got confused about this phenomenon . Can anyone of you give me some 
suggestions?

Thank you in advance.

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


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--


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


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[gmx-users] genbox -ci solute.gro -nmol N

[Chih-Ying Lin]

Hi

Originally, in the topol.top file =
[molecule]
solute 1


After the command:
genbox -cp one_solute.gro  -cs  spc216.gro -ci one_solute.gro  -nmol  N -p
topol.top
in the topol.top file =

[molecule]
solute 1
solvent 5000

I think the flag -p topol.top in the genbox command did not do it
correctly.
I am considering the two possible modification on the topol.top file
[molecule]
solute (1+N)
solvent 5000


[molecule]
solute (1+N)
solvent (5000 - N)

Which one is correct?
Or, none of them is correct?
What is the correct form of it?


Thank you
Lin
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Re: [gmx-users] genbox -ci solute.gro -nmol N

[Justin A. Lemkul]

Chih-Ying Lin wrote:



Hi

Originally, in the topol.top file =
[molecule]
solute 1


After the command:
genbox -cp one_solute.gro  -cs  spc216.gro -ci one_solute.gro  -nmol  N 
-p topol.top

in the topol.top file =

[molecule]
solute 1
solvent 5000

I think the flag -p topol.top in the genbox command did not do it 
correctly.

I am considering the two possible modification on the topol.top file
[molecule]
solute (1+N)
solvent 5000


[molecule]
solute (1+N)
solvent (5000 - N)

Which one is correct?


Depends, what's in the genbox output structure?


Or, none of them is correct?
What is the correct form of it?



It is often easier to insert a molecule with -ci, then solvate in the next step 
(at least from a conceptual standpoint).  I don't know how the code will handle 
it, but it should certainly clear up your confusion.


-Justin



Thank you
Lin












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--


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


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[gmx-users] Concentration

[Chih-Ying Lin]

Hi
How to make a solution with specific concentration ?

Command 1 =
editconf -d  0.75  -bt cubic
0.75=Distance between the solute and the box
cubic = the type of the simulation box


Command 2 =
genbox -cp solute.gro -cs spc.gro -box Y Y Y
Y = the box vector in nm

If I use cubic in my system, is Y defined as the length of the cubic in the
three directions?
Is the overall volume of the simulation box = Y * Y *Y  (nm*nm*nm) ?
Is the center of cubic on the origin (0,0,0) of the coordinate?


Thank you
Lin
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Re: [gmx-users] Concentration

[Justin A. Lemkul]

Chih-Ying Lin wrote:



Hi
How to make a solution with specific concentration ?



Concentration of what?  For ions, use genion -conc; for other solute molecules, 
do some simple stoichiometry from General Chemistry based on the box volume.



Command 1 =
editconf -d  0.75  -bt cubic
0.75=Distance between the solute and the box
cubic = the type of the simulation box


Command 2 =
genbox -cp solute.gro -cs spc.gro -box Y Y Y
Y = the box vector in nm

If I use cubic in my system, is Y defined as the length of the cubic in 
the three directions?


Yes, that's what you've instructed genbox to do.


Is the overall volume of the simulation box = Y * Y *Y  (nm*nm*nm) ?


Yes.


Is the center of cubic on the origin (0,0,0) of the coordinate?



No.  By convention, the system will be centered at (Y/2) in each direction.

If you're setting up your system using the above commands, it might be easier to 
just combine the box creation into one step with editconf (which will also print 
the coordinates of the system center): editconf -bt cubic -box Y -c


-Justin



Thank you
Lin









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--


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


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[gmx-users] problems running grompp with protein-ligand complex

[Ragnarok sdf]

I am working with a protein-ligand complex in gromacs with ffamber99
forcefield. I was able to generate the topology file for my ligand with
acpypi. Was also able to insert the ligand coordinates into my protein's
coordinate file. Was also able to generate the water box with genbox. The
number of molecules all match, the ligand coordinates are still there but
grompp tells me that:
Fatal error:
Found a second defaults directive, file ligand.itp, line 5
I've checked wikigromacs, but the solution given there, to simply erase the
second default line does not suit me here. Once I do this, i mean, go to my
ligand.itp file and put a ; before my default section, grompp does not
recognize anymore that my ligand is there and gives out another error line.
I would like some advice on the matter if possible.
Thank you in advance
Fabrício Bracht
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Re: [gmx-users] problems running grompp with protein-ligand complex

[Justin A. Lemkul]

Can you post the contents of your ligand.itp?

-Justin

Ragnarok sdf wrote:
I am working with a protein-ligand complex in gromacs with ffamber99 
forcefield. I was able to generate the topology file for my ligand with 
acpypi. Was also able to insert the ligand coordinates into my protein's 
coordinate file. Was also able to generate the water box with genbox. 
The number of molecules all match, the ligand coordinates are still 
there but grompp tells me that:

Fatal error:
Found a second defaults directive, file ligand.itp, line 5
I've checked wikigromacs, but the solution given there, to simply erase 
the second default line does not suit me here. Once I do this, i mean, 
go to my ligand.itp file and put a ; before my default section, grompp 
does not recognize anymore that my ligand is there and gives out another 
error line.

I would like some advice on the matter if possible.
Thank you in advance
Fabrício Bracht




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


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[gmx-users] no density option in g_energy

[Q. Y. HUAN]

Dear all, 
Why there is no density option when  I do g_energy amalyzation.
 
thanks

QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.


  
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Re: [gmx-users] no density option in g_energy

[Justin A. Lemkul]

Q. Y. HUAN wrote:
Dear all, 
Why there is no density option when  I do g_energy amalyzation.
 


This question was asked just a few weeks ago (hint: search the list for 
answers!).  Searching no density g_energy will lead you to this:


http://www.gromacs.org/pipermail/gmx-users/2008-November/037712.html

-Justin


thanks

QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.


  
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--


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


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[gmx-users] SMP/Parallel mdrun

[Ian Stokes-Rees]

I am a computational scientist working with a physical chemist to try to 
parallelize her use of gromacs -- today is my first day using the 
application and I am not succeeding in getting multiple threads.


I have an MPI-compiled version of gromacs v4.0 and am attempting to get 
parallel execution on a 2x2 core AMD Opteron system via:


$ lamboot
$ mdrun -np 4 -s ../1WOM.tpr -v -N 4

however there is then only a single thread executing.  Do I need to 
preprocess the topology file?


In the first instance, getting mdrun going in parallel on an SMP machine 
is the higher priority.  Next I will look at running it on a cluster.


TIA.

Ian

--
Ian Stokes-Rees, Research Associate
SBGrid, Harvard Medical School
http://sbgrid.org

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Re: [gmx-users] SMP/Parallel mdrun

[Mark Abraham]

Ian Stokes-Rees wrote:
I am a computational scientist working with a physical chemist to try to 
parallelize her use of gromacs -- today is my first day using the 
application and I am not succeeding in getting multiple threads.


Terminology - GROMACS is not threaded, but uses MPI processes for 
parallelism.


I have an MPI-compiled version of gromacs v4.0 and am attempting to get 
parallel execution on a 2x2 core AMD Opteron system via:


$ lamboot
$ mdrun -np 4 -s ../1WOM.tpr -v -N 4


-N does nothing, and -np is no longer accepted - as you'd know from 
reading mdrun -h, right?


Like most MPI parallel codes, you need to use mpirun. If your lam 
environment is correctly configured, then I think you will not need -np 
4 as an argument to mpirun.


Also, probably you are actually running a non-MPI gromacs, since by 
default, using --enable-mpi will suffix mdrun to be mdrun_mpi.


however there is then only a single thread executing.  Do I need to 
preprocess the topology file?


Not with gromacs 4.

Mark
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Re: [gmx-users] SMP/Parallel mdrun

[Ian Stokes-Rees]

Hi Mark,

Mark Abraham wrote:
Terminology - GROMACS is not threaded, but uses MPI processes for 
parallelism.


Yes, I gathered that.
I have an MPI-compiled version of gromacs v4.0 and am attempting to 
get parallel execution on a 2x2 core AMD Opteron system via:


$ lamboot
$ mdrun -np 4 -s ../1WOM.tpr -v -N 4


-N does nothing, and -np is no longer accepted - as you'd know from 
reading mdrun -h, right?
That is a bit of a condecending way of putting it. If I knew -N did 
nothing and -np was no longer accepted, then of course I would not have 
used them. In fact, I was reading the documentation from a file called 
manual-4.0.pdf which stated:



If you have a single machine with multiple processors you don’t have to 
use the mpirun com-

mand, but you can do with an extra option to mdrun:
% mdrun -np 8 -s topol -v -N 8


so that is where I took the example from. I think this PDF was linked 
from the gromacs documentation section of the website.


Like most MPI parallel codes, you need to use mpirun. If your lam 
environment is correctly configured, then I think you will not need 
-np 4 as an argument to mpirun.


Also, probably you are actually running a non-MPI gromacs, since by 
default, using --enable-mpi will suffix mdrun to be mdrun_mpi.

Doesn't look like it:

$ ./configure --prefix=/opt/osg-shared/se/app/site --with-pic --enable-mpi
$ make
$ make install
$ ls /opt/osg-shared/se/app/site/bin/ | grep mdrun
mdrun

Anyway, thanks for your suggestions because I now have it working via:

$ mpirun -np 4 /opt/osg-shared/se/app/site/bin/mdrun -s ../1WOM.tpr -v -N 4

and I see 4 processes running at 100% and an estimated run time 25% of 
the serial version.


Ian.

--
Ian Stokes-Rees, Research Associate
SBGrid, Harvard Medical School
http://sbgrid.org

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Re: [gmx-users] SMP/Parallel mdrun

[Mark Abraham]

Ian Stokes-Rees wrote:

Hi Mark,

Mark Abraham wrote:
Terminology - GROMACS is not threaded, but uses MPI processes for 
parallelism.


Yes, I gathered that.
I have an MPI-compiled version of gromacs v4.0 and am attempting to 
get parallel execution on a 2x2 core AMD Opteron system via:


$ lamboot
$ mdrun -np 4 -s ../1WOM.tpr -v -N 4


-N does nothing, and -np is no longer accepted - as you'd know from 
reading mdrun -h, right?
That is a bit of a condecending way of putting it. If I knew -N did 
nothing and -np was no longer accepted, then of course I would not have 
used them. In fact, I was reading the documentation from a file called 
manual-4.0.pdf which stated:



If you have a single machine with multiple processors you don’t have to 
use the mpirun com-

mand, but you can do with an extra option to mdrun:
% mdrun -np 8 -s topol -v -N 8


so that is where I took the example from. I think this PDF was linked 
from the gromacs documentation section of the website.


Hmmm that's been in the documentation since v3.3 and I've never seen 
code that might make it work. That looks like a documentation error.


Mark
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[gmx-users] Re: About entropic contribution to the potential of mean force

[Zhang Zhigang]

 I've got it! Thanks myself. ^_^
So, it seems that the prior calculations by, i.e. Ciccotti, et al, Chem.
Phys. 129, 241 (1989), Guardia, et al, J. Chem. Phys. 95, 2823 (1991) are
flawy since they have not corrected the entropic effects at all.

Cheers,

zgzhang


 Date: Wed, 26 Nov 2008 15:55:05 +0800
 From: Zhang Zhigang [EMAIL PROTECTED]
 Subject: [gmx-users] About entropic contribution to the potential of
meanforce
 To: gmx-users@gromacs.org
 Message-ID:
[EMAIL PROTECTED]
 Content-Type: text/plain; charset=iso-8859-1

 Hi,
In the manual of gromacs, the entropic contribution to the pmf is
 emphasized. In my opinion, this contribution is originated from the
 rotations of the constrained groups.
However, according to the manual suggestion, ...when calculating a PMF
 between two solutes in a solvent, for the purpose of simulating without
 solvent, the entropic contribution should be removed. I'm really confused
 with this.
If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl-
 and many water molecules), I want to calculate the potential of mean force
 of NaCl, should I count the contributions from the entropic effects?
According to Hess et al., (2006), JCP, 124: 164509, this effect should
 surely be added.
So, any one experienced with similar researches can give me an answer
 for this: when should I add the entropic contribution to the pmfs? and,
 what
 the really physical explanation for this effect?
Thanks in advance!

 Regards,

 zgzhang

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[gmx-users] Re: Re: Loss of bonds in HEME iron after pdb2gmx

[saradas]

Hi Justin,
Thanks a lot for the suggestions regarding the force field and the
sulphide bond. The bond is now formed after changing the distance range in
specbond.dat.
Thanks.
Sarada

 Message: 2
 Date: Wed, 26 Nov 2008 07:21:37 -0500
 From: Justin A. Lemkul [EMAIL PROTECTED]
 Subject: Re: [gmx-users] Re:  Loss of bonds in HEME iron after pdb2gmx
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: [EMAIL PROTECTED]
 Content-Type: text/plain; charset=UTF-8; format=flowed



 [EMAIL PROTECTED] wrote:
 Hi Justin,
 Thanks for your reply. I am using the gmx Gromacs Forcefield. As you
 said
 the topology file does contain the bonds and I need not have made the
 modificatins to specbond.dat. But using the original specbond.dat does
 not
 prevent the protonation of CYS. I renamed CYS as CYS2 in the input pdb
 file and used the following command line
 pdb2gmx_mpi -ignh -ff gmx -f 2c9_s50.pdb -o protein_h.pdb -p
 topology.top -water spce
 Am I  missing some crucial option here (like -ss for disulphide bonds)?
 Thanks once again.

 One piece of general advice - don't use ffgmx.  It has long been
 deprecated
 (according to the manual, the output of pdb2gmx, and dozens of posts on
 this
 list).  Use one of the newer Gromos96 force fields.

 Now, to address the actual question :)  The only thing I can think of is
 that
 specbond.dat uses a simple distance search to determine if the atoms are
 bonded,
 and I believe the tolerance is something like 10%.  So the value in
 specbond.dat
 of 0.25 implies that pdb2gmx should expect the S and Fe atoms to be 0.25
 +/- 0.2
 nm apart.  If they are much further apart, no bond will be detected.
 Check your
 input .pdb file to see how far apart these two atoms are.

 -Justin

 Regards,
 Sarada


 Message: 6
 Date: Tue, 25 Nov 2008 07:17:14 -0500
 From: Justin A. Lemkul [EMAIL PROTECTED]
 Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: [EMAIL PROTECTED]
 Content-Type: text/plain; charset=UTF-8; format=flowed



 [EMAIL PROTECTED] wrote:
 Hello,
 Sorry, I realised the HEME HEC naming was not the problem. But still
 the
 pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
 protonated and doesnot form a bond with HEME. I tried to preserve the
 bonds by editing the specbond.dat file. I do not know if it can be
 used
 for intramolecular bonding. Kindly inform if the modifications I have
 made
 are valid. The runtime information during the execution of pdb2gmx
 indicated the linking of FE in HEME to the N atoms. However, I do not
 see
 the bonds when I open the output file in Pymol. Please indicate how
 this
 problem can be resolved.

 Well, using visualization software may not indicate anything.  Most
 programs
 decide on bonds based on distance, not any sort of intelligent
 mechanism.
 The
 question is whether or not these bonds show up in your topol.top.

 This is the content of my specbond.dat file:

 5
 CYS SG  1   HEMEFE  5   0.25CYS HEME
 Well, this may be why your Cys is getting protonated - you're telling
 pdb2gmx
 that it should be!  See the format of specbond.dat here:

 http://wiki.gromacs.org/index.php/specbond.dat

 The second-to-last column should be the new residue name for cysteine,
 probably
 you want something like CYS2.

 HEMEFE  5   HEMENA  3   0.22HEMEHEME
 HEMEFE  5   HEMENB  3   0.22HEMEHEME
 HEMEFE  5   HEMENC  3   0.22HEMEHEME
 HEMEFE  5   HEMEND  3   0.22HEMEHEME

 Why is this section (above) even necessary?  Are these bonds not
 defined
 in the
 .rtp file of your force field?  Which force field are you using?  I
 know
 these
 are defined in the Gromos-type force fields.

 Try again with the original specbond.dat, but don't assume that
 visualization
 software will always indicate the presence/absence of a bond.  Examine
 your
 topology for that.

 -Justin

 And these I obtained during the execution of pdbgmx:

 Opening library file specbond.dat
 5 out of 5 lines of specbond.dat converted succesfully
 Special Atom Distance matrix:
   CYS122  CYS135  CYS143  CYS146  CYS150  CYS237
 CYS309
SG958  SG1059  SG1118  SG1136  SG1165  SG1902
 SG2475
   CYS135  SG1059   1.677
   CYS143  SG1118   1.076   1.092
   CYS146  SG1136   1.313   1.792   0.749
   CYS150  SG1165   1.175   2.054   0.978   0.426
   CYS237  SG1902   2.194   3.510   2.536   1.933   1.632
   CYS309  SG2475   1.745   2.703   2.469   2.507   2.423   2.449
   CYS343  SG2748   4.679   4.998   4.364   3.763   3.870   3.329
 4.426
   CYS406  SG3265   2.258   2.657   2.051   1.603   1.744   1.886
 2.198
   CYS457  SG3657   2.232   0.829   1.894   2.582   2.825   4.173
 2.898
  HEME462  FE3693   2.257   2.566   1.949   1.489   1.669   1.956
 2.343
  HEME462  NA3694   2.456   2.680   

Re: [gmx-users] no density option in g_energy

[Q. Y. HUAN]

Dear Justin, 
Thankk you very much for yr reply. I have forgotten that my system is under NVT 
condition. 
Thanks.

QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.


--- On Thu, 11/27/08, Justin A. Lemkul [EMAIL PROTECTED] wrote:

 From: Justin A. Lemkul [EMAIL PROTECTED]
 Subject: Re: [gmx-users] no density option in g_energy
 To: [EMAIL PROTECTED], Discussion list for GROMACS users 
 gmx-users@gromacs.org
 Date: Thursday, November 27, 2008, 9:22 AM
 Q. Y. HUAN wrote:
  Dear all, Why there is no density option when  I do
 g_energy amalyzation.
   
 
 This question was asked just a few weeks ago (hint: search
 the list for answers!).  Searching no density
 g_energy will lead you to this:
 
 http://www.gromacs.org/pipermail/gmx-users/2008-November/037712.html
 
 -Justin
 
  thanks
  
  QIU YI HUAN
  DEPARTMENT OF CHEMISTRY,
  FACULTY OF SCIENCE,
  UNIVERSITY PUTRA MALAYSIA,
  MALAYSIA.
  
  
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 http://www.gromacs.org/search before posting!
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 -- 
 
 Justin A. Lemkul
 Graduate Research Assistant
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 


  
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Re: [gmx-users] problems running grompp with protein-ligand complex

[Tsjerk Wassenaar]

Hi Fabrício,

 I've checked wikigromacs, but the solution given there, to simply erase the
 second default line does not suit me here. Once I do this, i mean, go to my
 ligand.itp file and put a ; before my default section, grompp does not
 recognize anymore that my ligand is there and gives out another error line.

Well, it's not like grompp is recognizing you have a ligand there
right now, is it? grompp doesn't reach the point where it realizes you
don't seem to have a ligand. It seems there's something wrong with the
topology. Better post ligand.itp, like Justin suggests, and also give
the error which occurs when you do comment out the defaults line in
the ligand topology.

Cheers,

Tsjerk

-- 
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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