date:20101019

[gmx-users] position_restraints

2010-10-19 Thread #ZHAO LINA#

Hi,

 Fatal error:
[ file protein.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section 
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.

Thanks for any clue. The part belongs to the one I want to restraints. I mean, 
the molecule is right.

Thanks,

lina
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[gmx-users] RE: Energy Minimization

2010-10-19 Thread Ehud Schreiber

Hi,

I would allow flexible water by uncommenting the line
define  = -DFLEXIBLE
and trying again; reducing the time step might also be required. 




Message: 4
Date: Mon, 18 Oct 2010 16:26:16 -0400
From: Sai Pooja 
Subject: [gmx-users] Energy Minimization
To: Discussion list for GROMACS users 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi all,

I am using CHARMM forcefield with tables for Protein SOL interactions
for
alanine dipeptide.
Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard
tables for 6-12 interactions used)
Combination rule changed from '2' to '1' in forcefield.itp file.

In the energy minimization step, using mdrun the following problem is
encountered:

Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps=1
   F-max =  2.98523e+10 on atom 4
   F-Norm=  1.32072e+09

step -1: Water molecule starting at atom 1149 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
title   = Energy Minimization   ; Title of run
; The following line tell the program the standard locations where to
find
certain files
cpp = /lib/cpp  ; Preprocessor
; Define can be used to control processes
;define  = -DFLEXIBLE
define  = -DPOSRES
; Parameters describing what to do, when to stop and what to save
integrator  = cg; Algorithm (steep = steepest descent
minimization)
emtol   = 1.0   ; Stop minimization when the maximum
force <
1.0 kJ/mol
nsteps  = 1 ; Maximum number of (minimization) steps
to
perform
nstenergy   = 1 ; Write energies to disk every nstenergy
steps
energygrps  = Protein SOL
energygrp_table = Protein SOL
; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions
ns_type = grid  ; Method to determine neighbor list
(simple,
grid)
coulombtype = User  ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
constraints = none  ; Bond types to replace by constraints
pbc = xyz   ; Periodic Boundary Conditions (yes/no)


Any suggestions?

Pooja


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Re: [gmx-users] g_dipole ? => Calculate bond dipole moment for a molecule of multiple atoms by hand?

2010-10-19 Thread Timo M.D. Graen

Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want 
to read the part about calculating dipole moments for an array of point 
charges, it is not difficult. 33 point charges are doable using pencil 
and calculator in about 10min. Do not worry about the reference point as 
long as your system is neutral, just set it to (0,0,0). Otherwise, take 
any kind of first year physics book it will contain very similar 
information.

On 10/19/2010 05:39 AM, Chih-Ying Lin wrote:

Hi
According to the following website,

http://en.wikipedia.org/wiki/Bond_dipole_moment

\mu = \delta \, d.
The bond dipole is modeled as +δ — δ- with a distance /d/ between the
partial charges  +δ and δ-.
For a complete molecule the total molecular dipole moment may be
approximated as the vector sum of individual bond dipole moments.

However, for a molecule of multiple atoms,
There may be more than one bond connected on one atom.
E
|
B - A - C
partial charge of atom_A = -0.5
partial charge of atom_B = 0.2
partial charge of atom_C = 0.35
partial charge of atom_E = 0.4

Which partial charges should I use when I calculate bond-dipole-moment
of A-B ?
Which partial charges should I use when I calculate bond-dipole-moment
of A-C ?
Which partial charges should I use when I calculate bond-dipole-moment
of A-E ?

Thank you
Lin

On 2010-10-18 03.30, Chih-Ying Lin wrote:

 HI
 I confined one molecule in the center of box and issue the g_dipole

command.

 The average dipole moment is still around 32.
 It is the molecule with 33 atoms / united atoms of most carbon groups,
 isn't the dipole moment around 32 too high?
 How can I test next and know that the dipole moment around 32 is
 acceptable?

By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you
have large charge separation you will get a large dipole.

 Thank you
 Lin
 On 2010-10-16 21.36, Chih-Ying Lin wrote:
 >
 > Hi
 > I issue the g_dipole command on Gromacs => And, the following
 > information is shown.
 > There are 10 molecules in the selection,
 > Does the Average =32.1611 refer to the average for a single over the
 > simulation time?
 > Or, the Average = 32.1611 summing for all the 10 molecules over the
 > simulation time?
 > If the average = 32.1611 for a single molecule with 33 atoms / united
 > atoms of most carbon groups, isn't the dipole moment too high?
 I think this is the average per molecule. You may need to run trjconv
 -pbc whole, because mdrun may break molecules in two parts, meaning that
 the molecule becomes as big as the box.

 >
 >
 >
 >
 > What does "will subtract their charge at their center of mass" this
 mean?
 > Why "will subtract their charge at their center of mass" ?
 >
 >
 >

--
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Computational Biomolecular Chemistry Group,
Am Fassberg 11
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Fax:  ++49 551 201 2302
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Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

2010-10-19 Thread ms


On 18/10/10 13:06, Mark Abraham wrote:

On 18/10/2010 10:53 PM, ms wrote:

On 18/10/10 03:30, Mark Abraham wrote:


Mark,

Thanks a lot for cc'ing me the bugzilla report. Do you think it is 
related to the problems I have? (well, for sure bugs can't help, but...)


thank you!

m.


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[gmx-users] Gibbs free energy of binding

2010-10-19 Thread shahab shariati

Hi gromacs users

Can I use gromacs for obtaining Gibbs free energy of binding of protein and
dna?
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[gmx-users] Gromacs libraries: same for both single and double precision builds?

2010-10-19 Thread Mark Dixon


Hi,

I'm installing GROMACS 4.5.1 on our Intel Nehalem/InfiniBand cluster and 
wish to install both single and double precision versions.


Am I correct in thinking that the same libraries are built, both with or 
without "--enable-double", and it's just the binaries that are different 
(and therefore all packaging issues are solved by use of the 
"--program-suffix" option)?


I'm planning on building both precisions in the same install - possibly 
with "--enable-shared" - and I want to double-check I can use the same 
library files.


Thanks,

Mark
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Re: [gmx-users] position_restraints

2010-10-19 Thread Justin A. Lemkul




#ZHAO LINA# wrote:

Hi,

 Fatal error:
[ file protein.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section 
"position_restraints"

in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.



As the error message indicates, your #include statement is in the wrong place. 
In the topology, order matters.  The [position_restraints] directive must be 
#included after the relevant [moleculetype] directive, and not after anything else.


-Justin

Thanks for any clue. The part belongs to the one I want to restraints. I 
mean, the molecule is right.


Thanks,

lina



--


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


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Re: [gmx-users] Gibbs free energy of binding

2010-10-19 Thread Justin A. Lemkul




shahab shariati wrote:

Hi gromacs users
 
Can I use gromacs for obtaining Gibbs free energy of binding of protein 
and dna?




Yes.  I would suggest you read about potential of mean force calculations.

-Justin

--


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


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[gmx-users] Re: for gromacs

2010-10-19 Thread Justin A. Lemkul



As I say continually, I am not a private tutor.  Please keep all Gromacs-related 
correspondence on the gmx-users list.  I am CC'ing this message there and would 
ask that any further discussion be held in this forum.


Binding energy is not trivial to calculate, and will require some type of free 
energy calculation (thermodynamic cycles, potential of mean force, etc). 
Breakdown of short-range nonbonded terms can be accomplished by using the 
"energygrps" keyword in the .mdp file.  If you've already done your simulation, 
you'll have to use the mdrun -rerun function with a new .tpr file that has these 
groups defined.


-Justin

rajender verma wrote:

dear sir
 I have done MD study of a complex compound (protein-Ligand). I want to 
calculate the Binding and breakdown energy with protein- ligand. pllease 
help me sir
 
Thanks


--
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Senior Research Fellow
National Institute of Pharmaceutical Education and Research (NIPER),
Sector - 67, S.A.S. Nagar. 160062, Punjab, INDIA
http://bioinfoindia.weebly.com/



--


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


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[gmx-users] Gibbs free energy of binding

2010-10-19 Thread chris . neale


Shahab,

Justin is entirely correct, you should read about potential of mean  
force calculations, the gromacs pull code, and the gromacs free energy  
code.


However, an important question is if you can *converge* the free  
energy of macromolecular binding. If you don't know the bound state,  
then I am sure that you can not. I think that it is even unlikely if  
you do know the bound state.


I suggest that you start by calculating the Gibbs free energy of a  
sodium ion binding to DNA. If you run the entire calculation in  
duplicate, but starting from different configurations, you should get  
a flavour of convergence difficulties and methods that you can apply  
to enhance your convergence.


Chris.

shahab shariati wrote:

Hi gromacs users
 Can I use gromacs for obtaining Gibbs free energy of binding of  
protein and dna?




Yes.  I would suggest you read about potential of mean force calculations.

-Justin


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[gmx-users] amb2gmx.pl script ignores negative values of PK?

2010-10-19 Thread Andrei Neamtu

Hi all,

There is a problem that I encountered when I was trying to manually
verify the proper dihedral conversion from AMBER topology to GROMACS
topology using amb2gmx perl script.
Some of the dihedrals were set to zero by amb2gmx even if in the
prmtop file they were not zero. This was happening for all the lines
that had PK with negative values!. Reading the script I came up with
the following lines for V[i] calculation (lines 749  to 755 in the
script file):

...

  # get all force constants for each line of a dihedral #
  my $lines = $i -1 +$numijkl;
  for(my $j=$i;$j<=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}>0) {
  $V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}

...

It seems from here that only PK values > 0 are considered when
computing the RB constants.
After I change the ">" sign to "!=" (i.e. not equal to) everything
goes fine and ALL the dihedral are transformed correctly.

While this is OK with different  AMBER sets and GAFF if one wish to
convert a GLYCAM (which comes also with Amber package) generated
topology, in the gromacs resultant file there will be missing
parameters for dihedrals. That's because GLYCAM does not use phase
shift and have also negative values for several PK

Is this a bug or there is a reason for considering only the positive
values of PK or I am missing something (as I am a begginer with
AMBER)?
(or maybe amb2gmx was designed only to work an AMBER ff conversion and
not for example GLYCAM)

Thanks for any comment,
Andrei
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[gmx-users] COM Pulling - Single Chain

2010-10-19 Thread C Johnson


Hi All,

I was wondering if it is possible to pull on a single chain?  I would like to 
anchor the C-terminus and pull the N-terminus and have a plot of pulling force 
vs displacement.

I'm looking for more or less a yes or no answer, if you would like to elaborate 
then I won't complain :)

Thanks,
Joe
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[gmx-users] COM Pulling - Single Chain

2010-10-19 Thread chris . neale


yes. use the pull code. check your convergence carefully.

--original message --

Hi All,

I was wondering if it is possible to pull on a single chain?  I would  
like to anchor the C-terminus and pull the N-terminus and have a plot  
of pulling force vs displacement.


I'm looking for more or less a yes or no answer, if you would like to  
elaborate then I won't complain :)


Thanks,
Joe

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[gmx-users] Umbrella sampling with temperature and pressure coupling method problem

2010-10-19 Thread DeChang Li

Dear all,

I want to use umbrella sampling to calculate the PMF of the
conformational transition of a protein. What temperature coupling method and
pressure coupling method should I use? Berendsen temperature coupling or
Nose-Hoover temperature coupling? Or each one is OK?
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[gmx-users] Umbrella sampling with temperature and pressure coupling method problem

2010-10-19 Thread chris . neale

Use Langevin dynamics (the sd integrator) to control the temperature.  
You are sure to get the correct ensemble that way and if you are doing  
US then you can not extract dynamics anyway.


Hopefully somebody else can address the pressure coupling for you, but  
probably you need to provide more information to get a useful answer  
there.


-- original message --

Dear all,

I want to use umbrella sampling to calculate the PMF of the
conformational transition of a protein. What temperature coupling method and
pressure coupling method should I use? Berendsen temperature coupling or
Nose-Hoover temperature coupling? Or each one is OK?


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Re: [gmx-users] mdrun-gpu error

2010-10-19 Thread Renato Freitas

Hi Roland,

I did as you suggested and it worked fine!

Thanks,

Renato


2010/10/15 Roland Schulz :
> You should use the latest GROMACS version also for the GPU. Thus compile the
> 4.5.1 for the GPU and run this.
>
> On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas  wrote:
>>
>> Hi there,
>> I have installed the gromacs-4.5.1 and it was running without
>> problems. Also I installed the GPU version of GROMACS
>> (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
>> NVIDIA driver are installed. Then I tried to run the test provided by
>> Alan with the mdrun-gpu and I got an error.
>>
>> # To test mdrun-gpu
>>
>> cat << EOF >| em.mdp
>> define                   = -DFLEXIBLE
>> integrator               = cg ; steep
>> nsteps                   = 200
>> constraints              = none
>> emtol                    = 1000.0
>> nstcgsteep               = 10 ; do a steep every 10 steps of cg
>> emstep                   = 0.01 ; used with steep
>> nstcomm                  = 1
>> coulombtype              = PME
>> ns_type                  = grid
>> rlist                    = 1.0
>> rcoulomb                 = 1.0
>> rvdw                     = 1.4
>> Tcoupl                   = no
>> Pcoupl                   = no
>> gen_vel                  = no
>> nstxout                  = 0 ; write coords every # step
>> optimize_fft             = yes
>> EOF
>>
>> cat << EOF >| md.mdp
>> integrator               = md-vv
>> nsteps                   = 1000
>> dt                       = 0.002
>> constraints              = all-bonds
>> constraint-algorithm     = shake
>> nstcomm                  = 1
>> nstcalcenergy            = 1
>> ns_type                  = grid
>> rlist                    = 1.3
>> rcoulomb                 = 1.3
>> rvdw                     = 1.3
>> vdwtype                  = cut-off
>> coulombtype              = PME
>> Tcoupl                   = Andersen
>> nsttcouple               = 1
>> tau_t                    = 0.1
>> tc-grps                  = system
>> ref_t                    = 300
>> Pcoupl                   = mttk
>> Pcoupltype               = isotropic
>> nstpcouple               = 1
>> tau_p                    = 0.5
>> compressibility          = 4.5e-5
>> ref_p                    = 1.0
>> gen_vel                  = yes
>> nstxout                  = 2 ; write coords every # step
>> lincs-iter               = 2
>> DispCorr                 = EnerPres
>> optimize_fft             = yes
>> EOF
>>
>> wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb
>>
>> pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce
>> -ignh
>>
>> editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0
>>
>> genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs
>>
>> grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr
>>
>> echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
>> Prot.top -norandom
>>
>> grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr
>>
>> mdrun -v -deffnm em
>>
>> grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr
>>
>> mdrun-gpu -v -deffnm md -device
>> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
>>
>> ---
>> Getting Loaded...
>> Reading file md.tpr, VERSION 4.5 (single precision)
>>
>> ---
>> Program mdrun-gpu, VERSION 4.5-GPU-beta2
>> Source code file:
>> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
>> line: 1971
>>
>> Fatal error:
>> reading tpx file (md.tpr) version 73 with version 71 program
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> I also have tried to use my own system to test the mdrun-gpu and I got
>> the same error.
>> Any ideas?
>>
>> Thanks,
>>
>> Renato
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Pleas

Re: [gmx-users] Umbrella sampling with temperature and pressure coupling method problem

2010-10-19 Thread Justin A. Lemkul




chris.ne...@utoronto.ca wrote:
Use Langevin dynamics (the sd integrator) to control the temperature. 
You are sure to get the correct ensemble that way and if you are doing 
US then you can not extract dynamics anyway.


Hopefully somebody else can address the pressure coupling for you, but 
probably you need to provide more information to get a useful answer there.




The Berendsen barostat suffers from the same limitations as the thermostat - the 
pressure distribution does not produce a true NPT ensemble.


-Justin


-- original message --

Dear all,

I want to use umbrella sampling to calculate the PMF of the
conformational transition of a protein. What temperature coupling method 
and

pressure coupling method should I use? Berendsen temperature coupling or
Nose-Hoover temperature coupling? Or each one is OK?




--


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


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Re: [gmx-users] COM Pulling - Single Chain

2010-10-19 Thread Warren Gallin

Maybe I'm confused here, but the manual says that the pull code will not in 
general work for groups that have other constraints.

To quote the last part of section 6.3:

There is one important limitation: strictly speaking, constraint forces can 
only be calculated between
groups that are not connected by constraints to the rest of the system. If a 
group contains
part of a molecule of which the bondlengths are constrained, the pull 
constraint and LINCS or
SHAKE bond constraint algorithms should be iterated simultaneously. This is not 
done in GROMACS.
This means that for simulations with constraints = all-bonds in the .mdp file
pulling is, strictly speaking, limited to whole molecules or groups of 
molecules. In some cases this
limitation can be avoided by using the free energy code, see sec. 6.4. In 
practice the errors caused
by not iterating the two constraint algorithms can be negligble when the pull 
group consists of a
large amount of atoms and/or the the pull force is small. In such cases the 
constraint correction
displacement of the pull group is small compared to the bond lengths.

So it sounds like you might be OK if you use a small pull force.

The free energy code is also problematic for measuring the forces because it 
creates a cycle of constraints, which yields an occasional but problematic 
spike to huge values when trying to calculate the free energy as a function of 
end-to-end distance of a peptide.

Warren Gallin

On 2010-10-19, at 6:50 AM, chris.ne...@utoronto.ca wrote:

> yes. use the pull code. check your convergence carefully.
> 
> --original message --
> 
> Hi All,
> 
> I was wondering if it is possible to pull on a single chain?  I would like to 
> anchor the C-terminus and pull the N-terminus and have a plot of pulling 
> force vs displacement.
> 
> I'm looking for more or less a yes or no answer, if you would like to 
> elaborate then I won't complain :)
> 
> Thanks,
> Joe
> 
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/625c900f/attachment.html
> 
> 
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[gmx-users] COM Pulling - Single Chain

2010-10-19 Thread Chris Neale


Warren,


You're right that one can not use constraints if they are also using lincs on 
C-C bonds.
However, constraining this bond is not necessary with a 1 fs timestep.

Even while constraining C-C bond lengths, one can still use harmonic restraints 
instead (also from the pull code).
Before getting any more specific replies, Joe will likely need to provide a 
whole bunch more information about what he
wants to do, what he has tried, what problem he has run into, etc.

Chris.

-- original message --

Maybe I'm confused here, but the manual says that the pull code will not in 
general work for groups that have other constraints.

To quote the last part of section 6.3:

There is one important limitation: strictly speaking, constraint forces can 
only be calculated between
groups that are not connected by constraints to the rest of the system. If a 
group contains
part of a molecule of which the bondlengths are constrained, the pull 
constraint and LINCS or
SHAKE bond constraint algorithms should be iterated simultaneously. This is not 
done in GROMACS.
This means that for simulations with constraints = all-bonds in the .mdp file
pulling is, strictly speaking, limited to whole molecules or groups of 
molecules. In some cases this
limitation can be avoided by using the free energy code, see sec. 6.4. In 
practice the errors caused
by not iterating the two constraint algorithms can be negligble when the pull 
group consists of a
large amount of atoms and/or the the pull force is small. In such cases the 
constraint correction
displacement of the pull group is small compared to the bond lengths.

So it sounds like you might be OK if you use a small pull force.

The free energy code is also problematic for measuring the forces because it 
creates a cycle of constraints, which yields an occasional but problematic 
spike to huge values when trying to calculate the free energy as a function of 
end-to-end distance of a peptide.

Warren Gallin


On 2010-10-19, at 6:50 AM,chris.neale at utoronto.ca  
  wrote:


/  yes. use the pull code. check your convergence carefully.

/>/
/>/  --original message --
/>/
/>/  Hi All,
/>/
/>/  I was wondering if it is possible to pull on a single chain?  I would like 
to anchor the C-terminus and pull the N-terminus and have a plot of pulling force 
vs displacement.
/>/
/>/  I'm looking for more or less a yes or no answer, if you would like to 
elaborate then I won't complain :)
/>/
/>/  Thanks,
/>/  Joe
/

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[gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)

2010-10-19 Thread DeChang Li

> Message: 6
> Date: Tue, 19 Oct 2010 09:30:47 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Umbrella sampling with temperature and
>pressurecoupling method problem
> To: Discussion list for GROMACS users 
> Message-ID: <4cbd9d87.6080...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> chris.ne...@utoronto.ca wrote:
> > Use Langevin dynamics (the sd integrator) to control the temperature.
> > You are sure to get the correct ensemble that way and if you are doing
> > US then you can not extract dynamics anyway.
> >
> > Hopefully somebody else can address the pressure coupling for you, but
> > probably you need to provide more information to get a useful answer
> there.
> >
>
> The Berendsen barostat suffers from the same limitations as the thermostat
> - the
> pressure distribution does not produce a true NPT ensemble.
>

   Whether the correct canonical ensemble (NPT or NVT) is important (or
indispensable) for umbrella sampling? If I used the weak coupling method
(Berendsen) to do the simulations, can I extract the PMF from the umbrella
sampling simulations?


>
> -Justin
>
> > -- original message --
> >
> > Dear all,
> >
> > I want to use umbrella sampling to calculate the PMF of the
> > conformational transition of a protein. What temperature coupling method
> > and
> > pressure coupling method should I use? Berendsen temperature coupling or
> > Nose-Hoover temperature coupling? Or each one is OK?
> >
> >
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
>
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[gmx-users] Point Dipoles

2010-10-19 Thread Donovan B.T.

Hi

Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole 
to a molecule with an orientation? I've looked in the manual but find nothing 
or online. Also is there any provision for SSD [soft sticky dipole] water 
molecules?

Thanks

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Re: [gmx-users] Point Dipoles

2010-10-19 Thread David van der Spoel


On 2010-10-19 18.40, Donovan B.T. wrote:

Hi

Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole 
to a molecule with an orientation? I've looked in the manual but find nothing 
or online. Also is there any provision for SSD [soft sticky dipole] water 
molecules?


No analytical dipoles. Would be nice to have.

Thanks

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Re: [gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)

2010-10-19 Thread Justin A. Lemkul

DeChang Li wrote:

Message: 6
Date: Tue, 19 Oct 2010 09:30:47 -0400
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Umbrella sampling with temperature and
   pressurecoupling method problem
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4cbd9d87.6080...@vt.edu >
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

chris.ne...@utoronto.ca  wrote:
 > Use Langevin dynamics (the sd integrator) to control the temperature.
 > You are sure to get the correct ensemble that way and if you are
doing
 > US then you can not extract dynamics anyway.
 >
 > Hopefully somebody else can address the pressure coupling for
you, but
 > probably you need to provide more information to get a useful
answer there.
 >

The Berendsen barostat suffers from the same limitations as the
thermostat - the
pressure distribution does not produce a true NPT ensemble.

   Whether the correct canonical ensemble (NPT or NVT) is important (or 
indispensable) for umbrella sampling? If I used the weak coupling method 
(Berendsen) to do the simulations, can I extract the PMF from the 
umbrella sampling simulations?

I would think that a proper statistical mechanical ensemble would be considered 
indispensable for any simulation.  In my mind, there is no real reason to use 
less accurate methods when collecting data.  If your goal is a comparison of 
methods, or consistency with other results, sure, then you may have a reason to 
use algorithms that may be less than optimal.  For any sensitive thermodynamic 
study, I would strongly argue that your potential energy surface needs to be 
rigorously correct.

The point is this.  You have to defend your choices to a skeptical audience 
(reviewers).  This is one question that might be asked, and really should be. 
Methods should be scrutinized.  So I would ask you this: why perform your 
simulations with algorithms that are not as accurate as others, when those 
better algorithms are accessible to you and do not harm performance in any 
demonstrable way?

-Justin

-Justin

 > -- original message --
 >
 > Dear all,
 >
 > I want to use umbrella sampling to calculate the PMF of the
 > conformational transition of a protein. What temperature coupling
method
 > and
 > pressure coupling method should I use? Berendsen temperature
coupling or
 > Nose-Hoover temperature coupling? Or each one is OK?
 >
 >

--

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

--

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

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[gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-19 Thread Kwee Hong

Hi,

I've got a top2psf.pl script from the web and used it to generate a psf file. 
Yet it generated  some bonds to atoms with index 0 which should not occur.  It 
causes VMD cannot load it and had a segmentation fault.  


vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
ERROR) Error reading bond information.
Segmentation fault

I wonder am I getting the right top2psf.pl.  Or is there any place I can get 
the 
latest stable version of that script? 


Here, I attached the perl script I used.

Thanks.

Regards,
Joyce




top2psf.pl
Description: Binary data
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Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-19 Thread Justin A. Lemkul




Kwee Hong wrote:

Hi,

I've got a top2psf.pl script from the web and used it to generate a psf 
file. Yet it generated  some bonds to atoms with index 0 which should 
not occur.  It causes VMD cannot load it and had a segmentation fault. 


vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
ERROR) Error reading bond information.
Segmentation fault

I wonder am I getting the right top2psf.pl.  Or is there any place I can 
get the latest stable version of that script?




There is only one version.  Zeros are only printed if something goes wrong, i.e. 
you have provided the wrong input or something else has failed.


Based solely on the information you've provided I cannot diagnose what has gone 
wrong.


-Justin


Here, I attached the perl script I used.

Thanks.

Regards,
Joyce



--


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


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Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-19 Thread Justin A. Lemkul

Kwee Hong wrote:

I executed the script at the therminal by typing
perl top2psf.pl -i topol.top -o zz.psf
Here, I attached my input file.

Your topology does not correspond to a MARTINI coarse-grained topology.  As 
such, probably a bunch of the pattern matching is getting incorrect information. 
 You cannot use top2psf.pl with this type of topology.  It was created for a 
very specific purpose and requires that format, nothing else.

-Justin

*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Wednesday, October 20, 2010 2:14:34
*Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms 
with index 0.

Kwee Hong wrote:
 > Hi,
 >
 > I've got a top2psf.pl script from the web and used it to generate a 
psf file. Yet it generated  some bonds to atoms with index 0 which 
should not occur.  It causes VMD cannot load it and had a segmentation 
fault.

 > vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
 > ERROR) Error reading bond information.
 > Segmentation fault
 >
 > I wonder am I getting the right top2psf.pl.  Or is there any place I 
can get the latest stable version of that script?

 >

There is only one version.  Zeros are only printed if something goes 
wrong, i.e. you have provided the wrong input or something else has failed.

Based solely on the information you've provided I cannot diagnose what 
has gone wrong.

-Justin

 > Here, I attached the perl script I used.
 >
 > Thanks.
 >
 > Regards,
 > Joyce
 >

-- 

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

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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Tables with forcefield

2010-10-19 Thread ms


On 27/09/10 21:18, Sai Pooja wrote:

Thanks M!

I am using the standard 6-12 tables available with the gromacs package. For
-table and -tablep options to start with.

I want to understand 1 thing. The forcefield files and the topology file
specifies sigma and epsilon parameters. If I change the combination rule to
1 in the forcefield.itp file, and use tables, how does gromacs convert the
sigma, epsilon values in the topology file to C6 and C12?


This is explained in the manual. specificially section 6.7.2



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[gmx-users] Template file in gromacs4.5.1

2010-10-19 Thread Sikandar Mashayak

Hi

I had developed couple of post processing/analysis codes in earlier version
of gromacs4.0.7.

Now I have upgraded to gromacs4.5.1 and when I check its template file , its
completely different that the earlier version. Does that mean old
post-processing codes have to rewritten if I were to use new gromacs?

thanks
sikandar
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[gmx-users] Re: Template file in gromacs4.5.1

2010-10-19 Thread Sikandar Mashayak

Also, will there be any errors if I use trajectory computed by gromacs4.5.1
and use post processing code developed for gromacs4.0.7. I plan to keep both
versions of gromacs installed on my system, until I get fully comfortable
new version!

On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak wrote:

> Hi
>
> I had developed couple of post processing/analysis codes in earlier version
> of gromacs4.0.7.
>
> Now I have upgraded to gromacs4.5.1 and when I check its template file ,
> its completely different that the earlier version. Does that mean old
> post-processing codes have to rewritten if I were to use new gromacs?
>
> thanks
> sikandar
>
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[gmx-users] Amber-GS-S force field in Gromacs 4.5.1

2010-10-19 Thread Lutz Maibaum

Hello all,

I noticed significant changes in my simulation results between running gromacs 
4.5.1 with the included amber-gs-s force field and gromacs 4.0.7 with Eric 
Sorin's amber ports. I eventually figured out that the parameter files in the 
amberGS.ff directory are identical (up to whitespace and comments) to those of 
the amber99sb force field. For example:

$ diff amberGS.ff/ffbonded.itp amber99sb.ff/ffbonded.itp 
366c366
< CK  CB  N*  CT   4  180.00 4.18400 2;
---
> CK  CBN*  CT   4  180.00 4.18400 2;

Is it possible that the parameter files got mixed up? If I understand 
correctly, amber-gs-s should be amber-94 without backbone dihedral potentials 
and without 1-4 scaling.

Thanks,

  Lutz

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[gmx-users] Re: Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul) (Justin A. Lemkul)

2010-10-19 Thread DeChang Li

>
>
>
> Message: 5
> Date: Tue, 19 Oct 2010 13:06:42 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and
>pressurecoupling method problem (Justin A. Lemkul)
> To: Discussion list for GROMACS users 
> Message-ID: <4cbdd022.6020...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> DeChang Li wrote:
> >
> >
> >
> > Message: 6
> > Date: Tue, 19 Oct 2010 09:30:47 -0400
> > From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
> > Subject: Re: [gmx-users] Umbrella sampling with temperature and
> >pressurecoupling method problem
> > To: Discussion list for GROMACS users  > >
> > Message-ID: <4cbd9d87.6080...@vt.edu  >>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > chris.ne...@utoronto.ca  wrote:
> >  > Use Langevin dynamics (the sd integrator) to control the
> temperature.
> >  > You are sure to get the correct ensemble that way and if you are
> > doing
> >  > US then you can not extract dynamics anyway.
> >  >
> >  > Hopefully somebody else can address the pressure coupling for
> > you, but
> >  > probably you need to provide more information to get a useful
> > answer there.
> >  >
> >
> > The Berendsen barostat suffers from the same limitations as the
> > thermostat - the
> > pressure distribution does not produce a true NPT ensemble.
> >
> >
> >Whether the correct canonical ensemble (NPT or NVT) is important (or
> > indispensable) for umbrella sampling? If I used the weak coupling method
> > (Berendsen) to do the simulations, can I extract the PMF from the
> > umbrella sampling simulations?
> >
>
> I would think that a proper statistical mechanical ensemble would be
> considered
> indispensable for any simulation.  In my mind, there is no real reason to
> use
> less accurate methods when collecting data.  If your goal is a comparison
> of
> methods, or consistency with other results, sure, then you may have a
> reason to
> use algorithms that may be less than optimal.  For any sensitive
> thermodynamic
> study, I would strongly argue that your potential energy surface needs to
> be
> rigorously correct.
>
> The point is this.  You have to defend your choices to a skeptical audience
> (reviewers).  This is one question that might be asked, and really should
> be.
> Methods should be scrutinized.  So I would ask you this: why perform your
> simulations with algorithms that are not as accurate as others, when those
> better algorithms are accessible to you and do not harm performance in any
> demonstrable way?
>
> -Justin
>

Thank you for your reply! So I will use Nose-Hoover for temperature
coupling and Parrinello-Rahman for pressure coupling in the data collection.
Anyway,  I may do some simulations with Berendsen method to see if there is
any difference in results when using the two coupling methods.


>
> >
> >
> > -Justin
> >
> >  > -- original message --
> >  >
> >  > Dear all,
> >  >
> >  > I want to use umbrella sampling to calculate the PMF of the
> >  > conformational transition of a protein. What temperature coupling
> > method
> >  > and
> >  > pressure coupling method should I use? Berendsen temperature
> > coupling or
> >  > Nose-Hoover temperature coupling? Or each one is OK?
> >  >
> >  >
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu  | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> >
> >
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
>
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[gmx-users] Error on install Gromacs 4

2010-10-19 Thread Son Tung Ngo

Dear experts,

I have just install gromacs 4.5.1 on my cluster (using CentOS that was
install openmpi1.5, Platform MPI, fftw3, g77, gcc , g++) but I have problem
with size of int :

[r...@icstcluster gromacs-4.5.1]# ./configure --prefix=/shared/apps/gromacs
--enable-mpi --enable-double
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the MPI cc command works... yes
checking for MPI_IN_PLACE in collective operations... yes
checking for catamount... no
checking how to run the C preprocessor... mpicc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether ln -s works... yes
checking whether mpicc accepts -O3... yes
checking whether mpicc accepts -msse2... yes
checking whether mpicc accepts -funroll-all-loops... yes
checking whether mpicc accepts -std=gnu99... yes
checking whether mpicc accepts -fexcess-precision=fast... no
checking whether mpicc accepts  -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes
checking whether byte ordering is bigendian... no
checking that size_t can hold pointers... yes
checking for SIGUSR1... yes
checking for pipes... yes
checking floating-point format... IEEE754 (little-endian byte and word
order)
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether mpicc accepts -g... yes
checking dependency style of mpicc... gcc3
checking how to run the C++ preprocessor... mpicc -E
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from mpicc object... failed
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3... yes
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking fo

[gmx-users] g_dipole ? => ionic bond => how to determine the direction of ionic bond dipole moment ?

2010-10-19 Thread Chih-Ying Lin

Hi
molecule dipole is 48.0 sum of q_i x_i
For a multiple-atoms molecule, the dipole moment of a covalent bond is a
vector, parallel to the bond axis,
For a multiple-atoms molecule, which includes a ionic bond, how to determine
the direction of ionic bond dipole moment in theory ?


How does Gromacs determine the direction of ionic bond dipole moment ?

Thank you
Lin








Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want
to read the part about calculating dipole moments for an array of point
charges, it is not difficult. 33 point charges are doable using pencil
and calculator in about 10min. Do not worry about the reference point as
long as your system is neutral, just set it to (0,0,0). Otherwise, take
any kind of first year physics book it will contain very similar
information.

On 10/19/2010 05:39 AM, Chih-Ying Lin wrote:
>
>
> Hi
> According to the following website,
>
> http://en.wikipedia.org/wiki/Bond_dipole_moment
>
>
> \mu = \delta \, d.
> The bond dipole is modeled as +δ -- δ- with a distance /d/ between the
> partial charges  +δ and δ-.
> For a complete molecule the total molecular dipole moment may be
> approximated as the vector sum of individual bond dipole moments.
>
>
> However, for a molecule of multiple atoms,
> There may be more than one bond connected on one atom.
> E
> |
> B - A - C
> partial charge of atom_A = -0.5
> partial charge of atom_B = 0.2
> partial charge of atom_C = 0.35
> partial charge of atom_E = 0.4
>
>
>
> Which partial charges should I use when I calculate bond-dipole-moment
> of A-B ?
> Which partial charges should I use when I calculate bond-dipole-moment
> of A-C ?
> Which partial charges should I use when I calculate bond-dipole-moment
> of A-E ?
>
> Thank you
> Lin
>
>
>
>
>
>
>
> On 2010-10-18 03.30, Chih-Ying Lin wrote:
>>  HI
>>  I confined one molecule in the center of box and issue the g_dipole
> command.
>>  The average dipole moment is still around 32.
>>  It is the molecule with 33 atoms / united atoms of most carbon groups,
>>  isn't the dipole moment around 32 too high?
>>  How can I test next and know that the dipole moment around 32 is
>>  acceptable?
> By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you
> have large charge separation you will get a large dipole.
>
>>  Thank you
>>  Lin
>>  On 2010-10-16 21.36, Chih-Ying Lin wrote:
>>  >
>>  > Hi
>>  > I issue the g_dipole command on Gromacs => And, the following
>>  > information is shown.
>>  > There are 10 molecules in the selection,
>>  > Does the Average =32.1611 refer to the average for a single over the
>>  > simulation time?
>>  > Or, the Average = 32.1611 summing for all the 10 molecules over the
>>  > simulation time?
>>  > If the average = 32.1611 for a single molecule with 33 atoms / united
>>  > atoms of most carbon groups, isn't the dipole moment too high?
>>  I think this is the average per molecule. You may need to run trjconv
>>  -pbc whole, because mdrun may break molecules in two parts, meaning that
>>  the molecule becomes as big as the box.
>>
>>  >
>>  >
>>  >
>>  >
>>  > What does "will subtract their charge at their center of mass" this
>>  mean?
>>  > Why "will subtract their charge at their center of mass" ?
>>  >
>>  >
>>  >
>
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[gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

2010-10-19 Thread Chih-Ying Lin

Hi
molecule dipole is 48.0 sum of q_i x_i
x_i the bond length for covalent bond.
but what is "x_i" for salt-molecule?


For salt-molecule, the ionic bonds are broken in water solvent and the
counter ions are spread among the water.

What is the "x_i" of the ionic bond in the dipole moment calculation?
Is x_i equal to the distance of the two parts of the salt-molecules (the
counter ion and the rest of the molecule) even though the salt molecule has
dissolved in the water?

I mean, is x_i equal to the length of simulation box if the counter ion and
the rest of the molecule are in the two sides of the simulation box?


I mean, if Gromacs takes x_i as the length of simulation box if the counter
ion and the rest of the molecule are in the two sides of the simulation box?

Thank you
Lin










Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want
to read the part about calculating dipole moments for an array of point
charges, it is not difficult. 33 point charges are doable using pencil
and calculator in about 10min. Do not worry about the reference point as
long as your system is neutral, just set it to (0,0,0). Otherwise, take
any kind of first year physics book it will contain very similar
information.

On 10/19/2010 05:39 AM, Chih-Ying Lin wrote:
>
>
> Hi
> According to the following website,
>
> http://en.wikipedia.org/wiki/Bond_dipole_moment
>
>
> \mu = \delta \, d.
> The bond dipole is modeled as +ä -- ä- with a distance /d/ between the
> partial charges <http://en.wikipedia.org/wiki/Partial_charges> +ä and ä-.
> For a complete molecule the total molecular dipole moment may be
> approximated as the vector sum of individual bond dipole moments.
>
>
> However, for a molecule of multiple atoms,
> There may be more than one bond connected on one atom.
> E
> |
> B - A - C
> partial charge of atom_A = -0.5
> partial charge of atom_B = 0.2
> partial charge of atom_C = 0.35
> partial charge of atom_E = 0.4
>
>
>
> Which partial charges should I use when I calculate bond-dipole-moment
> of A-B ?
> Which partial charges should I use when I calculate bond-dipole-moment
> of A-C ?
> Which partial charges should I use when I calculate bond-dipole-moment
> of A-E ?
>
> Thank you
> Lin
>
>
>
>
>
>
>
> On 2010-10-18 03.30, Chih-Ying Lin wrote:
>>  HI
>>  I confined one molecule in the center of box and issue the g_dipole
> command.
>>  The average dipole moment is still around 32.
>>  It is the molecule with 33 atoms / united atoms of most carbon groups,
>>  isn't the dipole moment around 32 too high?
>>  How can I test next and know that the dipole moment around 32 is
>>  acceptable?
> By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you
> have large charge separation you will get a large dipole.
>
>>  Thank you
>>  Lin
>>  On 2010-10-16 21.36, Chih-Ying Lin wrote:
>>  >
>>  > Hi
>>  > I issue the g_dipole command on Gromacs => And, the following
>>  > information is shown.
>>  > There are 10 molecules in the selection,
>>  > Does the Average =32.1611 refer to the average for a single over the
>>  > simulation time?
>>  > Or, the Average = 32.1611 summing for all the 10 molecules over the
>>  > simulation time?
>>  > If the average = 32.1611 for a single molecule with 33 atoms / united
>>  > atoms of most carbon groups, isn't the dipole moment too high?
>>  I think this is the average per molecule. You may need to run trjconv
>>  -pbc whole, because mdrun may break molecules in two parts, meaning that
>>  the molecule becomes as big as the box.
>>
>>  >
>>  >
>>  >
>>  >
>>  > What does "will subtract their charge at their center of mass" this
>>  mean?
>>  > Why "will subtract their charge at their center of mass" ?
>>  >
>>  >
>>  >
>
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Re: [gmx-users] Gibbs free energy of binding

2010-10-19 Thread mohsen ramezanpour

Dear Gromacs users

I want to calculate Gibbs free energy too,but about Protein-drug binding.
Please guide more clearly,what texts I need to read for learning how can I
do it?
Besides,g-energy has an option for estimating free energy from trajectory
file(-fee option)
I thought if I had a trajectory file of binding state I could estimate
binding free energy by this option.
am  I right?
does it give me Gibbs free energy?(Is this equall to binding free energy?)
thanks in advance
Mohsen

On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul  wrote:

>
>
> shahab shariati wrote:
>
>> Hi gromacs users
>>  Can I use gromacs for obtaining Gibbs free energy of binding of protein
>> and dna?
>>
>>
> Yes.  I would suggest you read about potential of mean force calculations.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

2010-10-19 Thread David van der Spoel

On 2010-10-20 06.06, Chih-Ying Lin wrote:

Hi
molecule dipole is 48.0 sum of q_i x_i
x_i the bond length for covalent bond.

No. x_i is the atomic position.

but what is "x_i" for salt-molecule?

For salt-molecule, the ionic bonds are broken in water solvent and the
counter ions are spread among the water.

What is the "x_i" of the ionic bond in the dipole moment calculation?
Is x_i equal to the distance of the two parts of the salt-molecules (the
counter ion and the rest of the molecule) even though the salt molecule
has dissolved in the water?

I mean, is x_i equal to the length of simulation box if the counter ion
and the rest of the molecule are in the two sides of the simulation box?

I mean, if Gromacs takes x_i as the length of simulation box if the
counter ion and the rest of the molecule are in the two sides of the
simulation box?

Thank you
Lin

Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want
to read the part about calculating dipole moments for an array of point
charges, it is not difficult. 33 point charges are doable using pencil
and calculator in about 10min. Do not worry about the reference point as
long as your system is neutral, just set it to (0,0,0). Otherwise, take
any kind of first year physics book it will contain very similar
information.

On 10/19/2010 05:39 AM, Chih-Ying Lin wrote:

 Hi
 According to the following website,

 http://en.wikipedia.org/wiki/Bond_dipole_moment

 \mu = \delta \, d.
 The bond dipole is modeled as +ä -- ä- with a distance /d/ between the
 partial charges <http://en.wikipedia.org/wiki/Partial_charges> +ä and ä-.
 For a complete molecule the total molecular dipole moment may be
 approximated as the vector sum of individual bond dipole moments.

 However, for a molecule of multiple atoms,
 There may be more than one bond connected on one atom.
 E
 |
 B - A - C
 partial charge of atom_A = -0.5
 partial charge of atom_B = 0.2
 partial charge of atom_C = 0.35
 partial charge of atom_E = 0.4

 Which partial charges should I use when I calculate bond-dipole-moment
 of A-B ?
 Which partial charges should I use when I calculate bond-dipole-moment
 of A-C ?
 Which partial charges should I use when I calculate bond-dipole-moment
 of A-E ?

 Thank you
 Lin

 On 2010-10-18 03.30, Chih-Ying Lin wrote:
>  HI
>  I confined one molecule in the center of box and issue the g_dipole
 command.
>  The average dipole moment is still around 32.
>  It is the molecule with 33 atoms / united atoms of most carbon groups,
>  isn't the dipole moment around 32 too high?
>  How can I test next and know that the dipole moment around 32 is
>  acceptable?
 By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you
 have large charge separation you will get a large dipole.

>  Thank you
>  Lin
>  On 2010-10-16 21.36, Chih-Ying Lin wrote:
> >
> > Hi
> > I issue the g_dipole command on Gromacs => And, the following
> > information is shown.
> > There are 10 molecules in the selection,
> > Does the Average =32.1611 refer to the average for a single over the
> > simulation time?
> > Or, the Average = 32.1611 summing for all the 10 molecules over the
> > simulation time?
> > If the average = 32.1611 for a single molecule with 33 atoms / united
> > atoms of most carbon groups, isn't the dipole moment too high?
>  I think this is the average per molecule. You may need to run trjconv
>  -pbc whole, because mdrun may break molecules in two parts, meaning that
>  the molecule becomes as big as the box.
>
> >
> >
> >
> >
> > What does "will subtract their charge at their center of mass" this
>  mean?
> > Why "will subtract their charge at their center of mass" ?
> >
> >
> >

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Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-19 Thread Kwee Hong

Alright.. 

I actually simulated my protein for 5ns. Then I loaded the trajectory file and 
.gro file in vmd. Then, I extracted one of the frame and write it into pdb 
format, When I open it with vmd, one of the atom from a residue is connected to 
another atom in another residue. Things like this happens as VMD uses a 
distance-based bond determination heuristic. Therefore, I would need a 
structure 
file which  specifies the bonds for my structure so that VMD doesn't have to 
guess.

So how can I generate the structure file I needed?

Thanks.

Regards,
Joyce

From: Justin A. Lemkul 
To: Gromacs Users' List 
Sent: Wednesday, October 20, 2010 2:25:26
Subject: Re: [gmx-users] top2psf.pl is generating some bonds to atoms with 
index 
0.

Kwee Hong wrote:
> I executed the script at the therminal by typing
> perl top2psf.pl -i topol.top -o zz.psf
> Here, I attached my input file.
> 

Your topology does not correspond to a MARTINI coarse-grained topology.  As 
such, probably a bunch of the pattern matching is getting incorrect 
information.  You cannot use top2psf.pl with this type of topology.  It was 
created for a very specific purpose and requires that format, nothing else.

-Justin

> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Wednesday, October 20, 2010 2:14:34
> *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with 
>index 0.
> 
> 
> 
> Kwee Hong wrote:
>  > Hi,
>  >
>  > I've got a top2psf.pl script from the web and used it to generate a psf 
>file. Yet it generated  some bonds to atoms with index 0 which should not 
>occur.  It causes VMD cannot load it and had a segmentation fault.
>  > vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
>  > ERROR) Error reading bond information.
>  > Segmentation fault
>  >
>  > I wonder am I getting the right top2psf.pl.  Or is there any place I can 
> get 
>the latest stable version of that script?
>  >
> 
> There is only one version.  Zeros are only printed if something goes wrong, 
>i.e. you have provided the wrong input or something else has failed.
> 
> Based solely on the information you've provided I cannot diagnose what has 
> gone 
>wrong.
> 
> -Justin
> 
>  > Here, I attached the perl script I used.
>  >
>  > Thanks.
>  >
>  > Regards,
>  > Joyce
>  >
> 
> -- 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- gmx-users mailing listgmx-users@gromacs.org 
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-- 

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

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