Re: [gmx-users] ci variable range error in parallel but NOT in serial

[David van der Spoel]

dtmirij wrote:

For the two processor job:

From my .mdp file, the pressure input data is as follows:

_
; Pressure coupling  =
Pcoupl   = Berendsen
Pcoupltype   = Anisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.0   1.0 1.0
compressibility  = 5e-6  5e-6  5e-6  0 0 0
ref_p= 1.0 1.0  1.0  1.0 1.0  1.0
__

The box info for the starting structure is as follows:
boxx=6.20239
boxy=6.81389
boxz=8.61949
__

at 20504.00 ps 
boxx=5.992789

boxy=6.585367
boxz=8.999877
__

I can't give the value of the box_lengths "right" before the crash as I
wrote out every 4 ps.

I am running a coarse grained lipid and water simulation DPPC/W

We need the whole box, not just one vector. However you can see that the 
box is deforming. You probably want an much longer tau_p. Nevertheless 
if your notation is right something may be fishy.


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Polarizability

[David van der Spoel]

Jones de Andrade wrote:

Hi list.

Well, a few days ago I've written a message concerning the future 
implementations that could be expected min gromacs 4 when it's released. 
Unfortunatelly, the thread hasn't gone any further.


lots of plans, but no promises. we really don't want to raise any 
expectations, more than significantly increased performance both 
sequential and parallel.




So, I would like to know if there is somone in this list who ever tried 
to modify gromacs program forces and energies routines. More 
specifically, if someone has tried to somehow implement any 
polarizability model in the force field, other than the "shells" model.


no plans. the shell model will most likely be the dominant model, both 
gromos and charmm developers are using it now.


if you feel like implementing other stuff yourself, you're welcome to 
continue the discussion on the developer list.


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Two polypeptides in one box

[Martin Höfling]

Am Samstag, 19. Mai 2007 schrieb Sheyore Omovie:

> I want to simulate interaction between two polypeptides in one box. I have
> read Tsjerk response to a similar question. However, i dont know just how
> to implement it, i.e how do I position two pdb files using editconf and
> create one pdb file. If possible I'll appreciate specific commands on how
> to implement this.

Depending on "how" you wanna align them, I would load them into PyMol (Swiss 
PDB Viewer ... ) and there, you can move, align, mutate ...

... and finally store as a pdb.
Then you can create a topology with pdb2gmx and so on.

Cheers
Martin
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Re: [gmx-users] Polarizability

[Jones de Andrade]

Hi David.

I had no idea that gromos was using it. Also, just had a few clues that
maybe charmm was. All amber clues however points towards a different model.

I have a few concerns about "directioning" (really sure that this is the
wrong word, if exists) that a shell model polarizability would make.
Absolutely no doubts that it would be probably faster than any iterative
model include dipoles, but I have this concern.

I'll be looking forward for the charmm papers on it (I've found the
references late this week) and try to compare its reproducibility and
parametrization methodologies somehow.

About implementing it: its a good idea, but a long term one. Basically it
means that nobody in the developer's list seems to be working on it righ
now, right?  ;)

Thanks a lot for all answers, David.  :)

Sincerally yours,

Jones

On 5/20/07, David van der Spoel <[EMAIL PROTECTED]> wrote:


Jones de Andrade wrote:
> Hi list.
>
> Well, a few days ago I've written a message concerning the future
> implementations that could be expected min gromacs 4 when it's released.
> Unfortunatelly, the thread hasn't gone any further.

lots of plans, but no promises. we really don't want to raise any
expectations, more than significantly increased performance both
sequential and parallel.

>
> So, I would like to know if there is somone in this list who ever tried
> to modify gromacs program forces and energies routines. More
> specifically, if someone has tried to somehow implement any
> polarizability model in the force field, other than the "shells" model.
>
no plans. the shell model will most likely be the dominant model, both
gromos and charmm developers are using it now.

if you feel like implementing other stuff yourself, you're welcome to
continue the discussion on the developer list.

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] What molecule generator should be used if using GROMOS Force Field?

[WU Yanbin]

Hi, Everyone,
 If I use GROMOS force field, what molecule generator, specially the
topology generation, should I use (just like for gromacs force field, there
is PRODRG)?
 I have tried to convert gromacs topology to GROMOS topology. The problem
is that some atom type like "CS2" in PEO does noe exist in GROMOS force
field. And GROMOS manual can not be downloaded for free. Where can I find
description for each atom type in GROMOS? Any suggestions? Thanks in
advance.
Yours Sincerely,
 WU Yanbin
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[gmx-users] pH

[Dmitriy Golubovsky]

Dear Guru!

have you got any idea, on what how to calculate pH. for the system?
i'm solving a promblem of coil-globule transition for polymer.
do the topology for my structure(opls ff), do MD in water (spc). get the
statiscts. everything is ok.
the summary charge is equal to zero. no dissociation.
so the question is - how to calculate pH. or it's not possible?
if it is possible, than how to variate this pH in some range.

I allready try to use genion, but didn't get good results, on case of very
big dependence of the results from the initial conformations of ions.

--
Dmitriy Golubovsky
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Re: [gmx-users] Polarizability

[David van der Spoel]

Jones de Andrade wrote:

Hi David.

I had no idea that gromos was using it. Also, just had a few clues that 
maybe charmm was. All amber clues however points towards a different model.


They have published a few paper on water and alcohols. The charm crew 
have done a few more. Amber is actually split into two IIRC, with point 
dipoles as well as shell models (that means either or).


I have a few concerns about "directioning" (really sure that this is the 
wrong word, if exists) that a shell model polarizability would make. 
Absolutely no doubts that it would be probably faster than any iterative 
model include dipoles, but I have this concern.
I think there is not a lot of difference, but shell models are easier to 
implement.




I'll be looking forward for the charmm papers on it (I've found the 
references late this week) and try to compare its reproducibility and 
parametrization methodologies somehow.


About implementing it: its a good idea, but a long term one. Basically 
it means that nobody in the developer's list seems to be working on it 
righ now, right?  ;)



I am working on shell models a bit (not enough...)



Thanks a lot for all answers, David.  :)

Sincerally yours,

Jones



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] pH

[David van der Spoel]

Dmitriy Golubovsky wrote:

Dear Guru!

have you got any idea, on what how to calculate pH. for the system?
i'm solving a promblem of coil-globule transition for polymer.
do the topology for my structure(opls ff), do MD in water (spc). get the 
statiscts. everything is ok.

the summary charge is equal to zero. no dissociation.
so the question is - how to calculate pH. or it's not possible?
if it is possible, than how to variate this pH in some range.

I allready try to use genion, but didn't get good results, on case of 
very big dependence of the results from the initial conformations of ions.



How about computing the H3O+ concentration?
It is close to impossible to simulate realistic pH with limited size 
systems. In practice your pH is always seven.


What do you mean with "no dissociation"?

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] What molecule generator should be used if using GROMOS Force Field?

[David van der Spoel]

WU Yanbin wrote:

Hi, Everyone,
  If I use GROMOS force field, what molecule generator, specially the 
topology generation, should I use (just like for gromacs force field, 
there is PRODRG)?
  I have tried to convert gromacs topology to GROMOS topology. The 
problem is that some atom type like "CS2" in PEO does noe exist in 
GROMOS force field. And GROMOS manual can not be downloaded for free. 
Where can I find description for each atom type in GROMOS? Any 
suggestions? Thanks in advance.



have you checked the gromos papers?

 Yours Sincerely,
  WU Yanbin




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] pH

[Erik Marklund]

20 maj 2007 kl. 20.59 skrev David van der Spoel:


Dmitriy Golubovsky wrote:

Dear Guru!
have you got any idea, on what how to calculate pH. for the system?
i'm solving a promblem of coil-globule transition for polymer.
do the topology for my structure(opls ff), do MD in water (spc).  
get the statiscts. everything is ok.

the summary charge is equal to zero. no dissociation.
so the question is - how to calculate pH. or it's not possible?
if it is possible, than how to variate this pH in some range.
I allready try to use genion, but didn't get good results, on case  
of very big dependence of the results from the initial  
conformations of ions.

How about computing the H3O+ concentration?
It is close to impossible to simulate realistic pH with limited  
size systems. In practice your pH is always seven.


Depending on your specific application, CPHMD can be used to simulate  
with constant pH. Unfortunately, CPHMD utilizes lambda-dynamics,  
which is not yet implemented in gromacs. It should not be THAT hard  
to implement yourself if you know a thing or two about MD and  
programing in general.


/Erik



What do you mean with "no dissociation"?

--
David.
__ 
__

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
 


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Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  +46 18 471 4537 fax: +46 18 511 755
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[gmx-users] Re: gmx-users Digest, Vol 37, Issue 73

[Dmitriy Golubovsky]

From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Date: Sun, 20 May 2007 20:59:45 +0200
Subject: Re: [gmx-users] pH
Dmitriy Golubovsky wrote:
> Dear Guru!
>
> have you got any idea, on what how to calculate pH. for the system?
> i'm solving a promblem of coil-globule transition for polymer.
> do the topology for my structure(opls ff), do MD in water (spc). get the
> statiscts. everything is ok.
> the summary charge is equal to zero. no dissociation.
> so the question is - how to calculate pH. or it's not possible?
> if it is possible, than how to variate this pH in some range.
>
> I allready try to use genion, but didn't get good results, on case of
> very big dependence of the results from the initial conformations of
ions.
>
How about computing the H3O+ concentration?
It is close to impossible to simulate realistic pH with limited size
systems. In practice your pH is always seven.

What do you mean with "no dissociation"?

Dear David,

thanks for a quick answer.
1. what do you mean, when you say "pH is always seven".
2. when I said "dissociation", I mean that, I didn't use Morse potential for
the bond, so, for examle, COOH group haven't got probability to break the
connectivity with H atom.
3. i haven't got an idea how to calculate H3O+ concentration.

Thanks.


--
Dmitriy Golubovsky
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Re: [gmx-users] Re: gmx-users Digest, Vol 37, Issue 73

[David van der Spoel]

Dmitriy Golubovsky wrote:



From: David van der Spoel <[EMAIL PROTECTED]
>
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Date: Sun, 20 May 2007 20:59:45 +0200
Subject: Re: [gmx-users] pH
Dmitriy Golubovsky wrote:
 > Dear Guru!
 >
 > have you got any idea, on what how to calculate pH. for the system?
 > i'm solving a promblem of coil-globule transition for polymer.
 > do the topology for my structure(opls ff), do MD in water (spc).
get the
 > statiscts. everything is ok.
 > the summary charge is equal to zero. no dissociation.
 > so the question is - how to calculate pH. or it's not possible?
 > if it is possible, than how to variate this pH in some range.
 >
 > I allready try to use genion, but didn't get good results, on case of
 > very big dependence of the results from the initial conformations
of ions.
 >
How about computing the H3O+ concentration?
It is close to impossible to simulate realistic pH with limited size
systems. In practice your pH is always seven.

What do you mean with "no dissociation"?

Dear David,
thanks for a quick answer.
1. what do you mean, when you say "pH is always seven".
2. when I said "dissociation", I mean that, I didn't use Morse potential 
for the bond, so, for examle, COOH group haven't got probability to 
break the connectivity with H atom.

3. i haven't got an idea how to calculate H3O+ concentration.

supposedly you know what you have in your system, and since you won't 
have any bonds breaking you can compute any concentration you like. 
since you most likely have zero H3O+ and zero OH- the pH is then that of 
a neutral system.

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] pH

[Miguel Machuqueiro]

>
> 20 maj 2007 kl. 20.59 skrev David van der Spoel:
>
>> Dmitriy Golubovsky wrote:
>>> Dear Guru!
>>> have you got any idea, on what how to calculate pH. for the system?
>>> i'm solving a promblem of coil-globule transition for polymer.
>>> do the topology for my structure(opls ff), do MD in water (spc).
>>> get the statiscts. everything is ok.
>>> the summary charge is equal to zero. no dissociation.
>>> so the question is - how to calculate pH. or it's not possible?
>>> if it is possible, than how to variate this pH in some range.
>>> I allready try to use genion, but didn't get good results, on case
>>> of very big dependence of the results from the initial
>>> conformations of ions.
>> How about computing the H3O+ concentration?
>> It is close to impossible to simulate realistic pH with limited
>> size systems. In practice your pH is always seven.
>
> Depending on your specific application, CPHMD can be used to simulate
> with constant pH. Unfortunately, CPHMD utilizes lambda-dynamics,
> which is not yet implemented in gromacs. It should not be THAT hard
> to implement yourself if you know a thing or two about MD and
> programing in general.

If you are interested in Constant-pH methods, you can take a look at:

Machuqueiro, M., Baptista, A.M. (2006) “Constant-pH Molecular Dynamics
with ionic strength effects: The protonation–conformation coupling in
decalysine”, J. Phys. Chem. B, 110, 2927-2933.

and several references therein.

And... as a reminder, our method is implemented with Gromacs.

Miguel Machuqueiro
ITQB-Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Molecular Simulation Group - 6º Floor
Av. da República, EAN, Apartado 127
2781-901 Oeiras, Portugal


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[gmx-users] Re: Calculate individual force between each atom pair

[WU Yanbin]

 Thanks for the suggestions.
 I have traced the calling sequence from do_force() to calculate LJ forces:
do_force() -->force() -->do_nonbonded(). But in do_nonbonded() function of
nonbonded.c file, if for general processor, it should have call
gmx_nb_generic_kernel() function but this line is in fact commented and the
implimentation of gmx_nb_generic_kernel() can not be found. My gromacs
version is v3.3.
 So is there previous implementation of this function? I can write it
myself but the efficiency will be much lower. Any suggestions? Thanks in
advance.
   Yours Sincerely,
 WU Yanbin
--



Message: 4
Date: Fri, 18 May 2007 09:14:22 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Calculate individual force between each atom
pair
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

WU Yanbin wrote:
> Hi, Everyone,
>   The force given by .trr file is the total force acted on each atom.
> Now I would like to modify codes to calculate individaul force between
> each atom pair. Is it possible in gromacs? (Because I remember some part
> of gromacs is writen in Fortran and already compiled).

Err, no, not Fortran. The inner loops for calculating energies and
forces are written in assembly for some common architectures, and there
are fall-back routines in C. It would not be too hard to modify these C
routines to write the nonbonded force between pairs of atoms in the
inner loops. Writing that to output is likely to be unreasonably slow,
and generate an unreasonably large data size (it's effectively a
trajectory of size N^2 now). Depending on your application you might not
need to write the numbers to a file, but you haven't told us what you
want here.

In any case, think very carefully about what you want to do, and then be
prepared to understand the whole structure of mdrun, and lots of fine
detail inside do_force()

Mark


--

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Re: [gmx-users] pH

[Mark Abraham]

Dmitriy Golubovsky wrote:

Dear Guru!

have you got any idea, on what how to calculate pH. for the system?
i'm solving a promblem of coil-globule transition for polymer.
do the topology for my structure(opls ff), do MD in water (spc). get the 
statiscts. everything is ok.

the summary charge is equal to zero. no dissociation.
so the question is - how to calculate pH. or it's not possible?
if it is possible, than how to variate this pH in some range.


Try thinking about this problem realistically. You have a simulation 
volume that's something like a cube with side length of few tens of nm. 
Do some numbers and work out what order of magnitude of such cubes you'd 
need to have one H3O+, so as to correspond to a 
experimentally-measurable non-seven pH.


Mark
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Re: [gmx-users] Polarizability

[Jones de Andrade]

Hi David

They have published a few paper on water and alcohols. The charm crew

have done a few more. Amber is actually split into two IIRC, with point
dipoles as well as shell models (that means either or).



I've found two papers for charmm polariability. But I'll only be able to try
to find it in the library or to ask for the authors tomorrow at least. But
thanks for the information!  ;)

On the other hand, I could not yet find any published material from amber
using shell models. Is this only an "inside group" discussion?

I think there is not a lot of difference, but shell models are easier to

implement.



I think too. In reality, there is no "visible rational reason" for this fear
of me, is more like a "feeling", so I'll try to find something more on it.

But I do agree that it's much likely that the shell model is much easier to
implement, if not faster to execute also. :)

I am working on shell models a bit (not enough...)


Me too. Specially cause this is long terms plans (2+ years from now).

But thanks a lot for all information, David. Helped a lot.

Sincerally yours,

Jones
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[gmx-users] readxtc can not get coordinates without jump?

[Hu Zhongqiao]

Hi,
 
I faced one problem when reading xtc file.
 
Assuming my xtc file is run.xtc and the last frame no. is 1 (time
step=1ps, e.g, 10 ns in total), I want to see the coordinates of the
whole system without jump at frame=1, and I used the command:
 
(1)trjconv -f run.xtc -s run.tpr -o sys_1.pdb -b 1 -e 1 -pbc
nojump
 
That is no problem, of course.
 
But I thought I could also do the same thing by 2 steps as follows:
 
(2.1)  first convert run.xtc to run_nojump.xtc (using -pbc nojump)
trjconv -f run.xtc  -s run.tpr -o run_nojump.xtc -pbc nojump
 
(2.2) use trjconv again to extract coordinates of system at frame=1
from run_nojump.xtc ( I thought I didnt need to use flag -pbc nojump in
this case)
trjconv -f run_nojump.xtc -s run.tpr -o sys_1.pdb -b 1 -e 1
But it is strange that some coordinates by 2 ways are different. It
seems that something wrong happened in step2.2 by checking the
coordinates.
 
But when I add flag -pbc nojump for the step 2.2
trjconv -f run_nojump.xtc -s run.tpr -o sys_1.pdb -b 1 -e 1
-pbc nojump
It does work.
 
Did anyone meet the same problem and give a reasonable explanation? 
 
In fact, I want to read coordinates of some particles without jump to
get the Mean Square Displacement (MSD). I used readxtc, a Fortran Code,
to get it, by linking xdr library, which is suggested by Gromacs
developers. But when readxtc read run_nojump.xtc, it can not give the
correct coordinates without jump, similar to what I said above. Then any
method to make a suitable xtc file which allow readxtc to get out
coordinates without jumps? Or after first coordinates with jump are read
out using readxtc, how can I convert them into those without jump in my
Fortran code?
 
By the way, I need to extract coordinates of some particles satisfying
some specific conditions and these particle changes from one frame to
another frame, so some availabe analysis commands cannot do this
conveniently. 
 
Zhongqiao Hu
 
 
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