Re: [gmx-users] Distance for window spacing in US?

[Andrei Neamtu]

Hi,
As i understand, if pulling geometry is set to  'pull_geometry = distance'
and 'pull_dim = Y Y Y" then the DISTANCE between the COM of the enzyme and
the ligand is restrained with the umbrella potential. If using long enough
simulation times for each restraint umbrella window, as long as the ligand
leaves the binding site it can freely diffuse in the space around the
enzyme as only the distance between COMs is restrained, is this correct?
And if using let's say 'pull_dim = Y N N' it can freely diffuse away in the
YZ plane while keeping to a certain extent the X distance constant in each
window. Is there a way to stop this diffusion to let the ligand move only
on X direction?
Maybe I put a trivial question (sorry for this :) ) but I cannot see why
restraining only in one direction let's say X if the ligand will diffuse in
the YZ plane? I'm facing the same problem with a host - guest complex. I
tried both the 'pull_dim = Y Y Y' (and the guest started to diffuse around
the host after a certain distance, 4 ns on each window) and 'pull_dim = N N
Y' ( and the guest diffused in the XY plane).
But, in principle .. the free energy being a state function it does not
matter which way the process of dissociation takes place as long as you
pull away to sufficient distance the ligand  from the host (or enzime),
considering of course the distance between the COMs as the reaction
coordinate. This of course if one is interested only in the free energy
variation.

Best regards,

Andrei

On Fri, Feb 22, 2013 at 10:33 AM, Erik Marklund wrote:

>
> On Feb 22, 2013, at 1:13 AM, Justin Lemkul wrote:
>
>
>> On 2/21/13 6:24 PM, Yun Shi wrote:
>>
>>> So in umbrella sampling, does it really matter if the vector
>>> connecting the COMs of protein and ligand is NOT parallel with the
>>> vector of the pulling force (although the pull rate is 0)?
>>>
>>> I guess as long as the force in each sampling window is along the same
>>> direction, we can in theory get potential of mean force along any
>>> direction.
>>>
>>>
>> I honestly don't know how that would affect things.  Perhaps someone else
>> who has dealt with such cases can comment, but typically it is easiest to
>> define the reaction coordinate to be coincident with the direction(s) along
>> which you wish to apply the umbrella restraint.
>>
>> -Justin
>>
>
> The important thing is that your PMF is calculated along a sensible
> reaction coordinate. In the worst case there may be free energy barriers
> perpendicular to your coordinate which the system would have to cross.
> Those will be important for the kinetics and thermodynamics that you aim to
> study, but will not appear in your PMF.
>
> Erik
>
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[gmx-users] amb2gmx.pl script ignores negative values of PK?

[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] mk_angndx

[Andrei Neamtu]

Hi all,

I am trying to make a PCA analysis of an protein md trajectory in
dihedral space. Anyway I don't really understand how to use mk_angndx
. When I run this command:

mk_angndx -s ../foo.tpr -n dangle.ndx -type ryckaert-bellemans

it seems that the resulting index file contains all the dihedrals in
the tpr structure file grouped by the force constant of the first
Ryckaert-Bellemans coefficient, but I want only the phi-psi dihedrals.

Is there a way of doing this?

Thanks,
Andrei


 
 Dr. Andrei Neamtu, PhD, Lecturer
 Dept. of Physiology
"Gr. T. Popa" Iasi University of Medicine and Pharmacy
 http://www.umfiasi.ro/
 str. Universitatii nr. 16
 IASI, Jud. Iasi
 ROMANIA
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Re: [gmx-users] free energy landscape question

[Andrei Neamtu]

Dear Antonio,
thank you.
I think I got the idea. I need to use a cut-off for the probability:
for all the probabilities lower than a certain value I assign to them
that (lower) value so the energy will be constant.

Thanks,
Andrei

On Wed, Jun 23, 2010 at 8:49 PM,   wrote:
>
> On Wed, 23 Jun 2010, Andrei Neamtu wrote:
>
>> Dear Andreas and Marc,
>> Thanks for your reply.
>> I am not familiar with the gromacs programming code and so I am trying
>> to build myself the FEL.
>> I can generate the hisotgram of the number of states from the
>> projection along principal component 1 and 2 (PC1 and PC2) using
>> SigmaPlot but here I am stucked!
>>
>> I think that I have to compute the free energy with the formula G = -
>> kT ln(Pi/Pmax) where Pi is the probability of the state i (determined
>> py a certain pair of values of PC1 and PC2) and Pmax is the maximum
>> probability. But for certain there are regions in the principal
>> component plane with probabiliy zero which constitutes singularities
>> for the above formula (infinite energy).
>
> Hi Andrei,
>
> You can simply assign to those regions a very high energy value (e.g.,
> 100RT) that works as "+infinite". In practice, this doesn't matter, since
> you will always use an energy cutoff much lower than that when plotting or
> projecting your landscape.
>
>> From my experience, you should also pay attention to the choice of bin
>
> size and the eventual use of smoothing methods, especially if you are
> thinking about going to 3D or higher-dimensional histograms. We ended up
> using kernel density estimates instead of histograms
> (http://dx.doi.org/10.1021/jp902991u).
>
> Have a nice landscaping,
> Antonio
>
>>
>> Any ideas?
>>
>> Many thanks,
>> Andrei
>>
>> On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink
>>  wrote:
>>>
>>> On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:
>>>>
>>>> Yes, that is an interesting question. I don't know the answer, but is
>>>> there any way to get the numerical values of the matrix from Gromacs tools
>>>> that produce a matrix in xpm format ? I have problems with g_rms and
>>>> g_rmsdist is another candidate.
>>>
>>> probably the easiest is to look at the code and print out the matrix
>>> before it's sent to the xpm plotting routine.
>>>
>>> you can also convert the xpm afterwards, but I guess the data then
>>> gets quantized.
>>>
>>> cheers,
>>> marc
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>
> --
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> Av. da Republica - EAN
> 2780-157 Oeiras, Portugal
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Re: [gmx-users] free energy landscape question

[Andrei Neamtu]

Dear Andreas and Marc,
Thanks for your reply.
I am not familiar with the gromacs programming code and so I am trying
to build myself the FEL.
I can generate the hisotgram of the number of states from the
projection along principal component 1 and 2 (PC1 and PC2) using
SigmaPlot but here I am stucked!

I think that I have to compute the free energy with the formula G = -
kT ln(Pi/Pmax) where Pi is the probability of the state i (determined
py a certain pair of values of PC1 and PC2) and Pmax is the maximum
probability. But for certain there are regions in the principal
component plane with probabiliy zero which constitutes singularities
for the above formula (infinite energy).

Any ideas?

Many thanks,
Andrei

On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink
 wrote:
> On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:
>> Yes, that is an interesting question. I don't know the answer, but is there 
>> any way to get the numerical values of the matrix from Gromacs tools that 
>> produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is 
>> another candidate.
>
> probably the easiest is to look at the code and print out the matrix
> before it's sent to the xpm plotting routine.
>
> you can also convert the xpm afterwards, but I guess the data then
> gets quantized.
>
> cheers,
> marc
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[gmx-users] free energy landscape question

[Andrei Neamtu]

Hi,

I am trying to use g_sham to obtain free energy landscape from a simulation.
I can obtain the .xpm files but I want to know if there is any way of
obtaining the actual histogram (in a form of a ASCII matrix vith
numerical values) to use it in some other plotting program to draw
contour lines plots of the surface

Many thanks,
Andrei
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[gmx-users] free energy landscape question

[Andrei Neamtu]

Hi,

I am trying to use g_sham to obtain free energy landscape from a simulation.
I can obtain the .xpm files but I want to know if there is any way of
obtaining the actual histogram (in a form of a ASCII matrix vith
numerical values) to use it in some other plotting program to draw
contour lines plots of the surface

Many thanks,
Andrei
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Re: [gmx-users] question about compass ff

[Andrei Neamtu]

Justin, thank you.

In fact I am worried about the cross coupling terms which apper i the
functional form of COMPASS and CVFF.

As far as I know in GROMACS there are no such terms, so I am asking if
there might be a solution to include these by editing .itp, nb.itp,
bon.itp, .rtp, etc, without the need to modify the gromacs CODE.

Andrei

On Wed, Jun 2, 2010 at 2:23 PM, Justin A. Lemkul  wrote:
>
>
> Andrei Neamtu wrote:
>>
>> Dear all,
>>
>> does anyone know if it is possible to somehow use COMPASS or CVFF
>> forcefields in Gromacs?
>>
>
> You can probably implement just about anything by creating the right files
> (.itp, nb.itp, bon.itp, .rtp, etc).  Quite a bit of work, but not too
> conceptually difficult.  Whether or not there need to be changes to the
> source code to accommodate new force fields may be another issue.
>
> -Justin
>
>> Thanks,
>> Andrei
>
> --
> 
>
> 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] question about compass ff

[Andrei Neamtu]

Dear all,

does anyone know if it is possible to somehow use COMPASS or CVFF
forcefields in Gromacs?

Thanks,
Andrei
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Re: [gmx-users] rmsf question

[Andrei Neamtu]

Hi,
thank you all.

I have asked the question about RMSD because of the following reason:

I simulate a protein whose structure was determined by NMR only.
My simulation is quite long (2 microseconds) in the absence of a
ligand, present in the experimental structure file. During the course
of the simulation the protein simulated is subjected to large
conformational tranitions.
To validate the results I also have made a simulation (also 2
microseconds) with the ligand present which I expected to preserve the
original protein conformation.
This is indeed happening for 300 nanoseconds after which a
reorganisation of secondary  structure elements takes place. This is
happening in my opinion due to the fact that my simulation is at the
physiological temperature of 310K while the NMR structure was resolved
at 293K.
Now I am repeating the second simulation at 293K.
To evaluate the accuracy of the simulations I want to compare the data
in the simulation with ligand bound, to as much experimental data as
possible. NMR experiments provide data that can be used to bencmark
the accuracy of simulations.
So, I thought that locally (on short time scale, under 1 nanosecond)
the RMS fluctuations of the C-alpha of the backbone can be correlated
to RMSF of the bundle of conformations in the NMR file. This now seems
to me that it doesn't make sense. So I wil try to use the backbone
order parameters for comparison.

Andrei

On Tue, Mar 16, 2010 at 11:50 AM, Tsjerk Wassenaar  wrote:
> Hi Andrei,
>
>> If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
>> structure, is a measure of the uncertanty in resolving the structure.
>
> No, that's not what I said. You're saying that there's one structure
> (the structure), but there is uncertainty in resolving it. That's not
> the case. There is a distribution of structures that gives rise to a
> set of signals, from which time and ensemble averaged distances
> between certain pairs of atoms can be deduced. But this set of
> distances is typically leaves a number of degrees of freedom, and on
> top of that the time averaging may actually yield restraints that
> cannot be satisfied simultaneously. So, structures have to be fit to
> the set of distances, which is typically repeated a large number of
> times using simulated annealing with different starting conditions.
> >From the resulting set the ones best fitting the data are selected and
> put forward as a representative set of structures. The least defined
> regions, in terms of (distance) restraints are likely to show most
> variation. But the structures are not weighted according to their
> probabilities and therefore neither the average nor the fluctuations
> can be expected to coincide with the moments of the Boltzmann
> distribution.
>
>> Compared to this the RMSF of C-alpha computed from a MD trajectory
>> reflects the geometric fluctuations of the backbone in the Boltzmann
>> distribution of states in the generated ensemble.
>
> Assuming you have sampled long enough and not just trying to explain
> drift as fluctuation :)
>
>> The uncertanty in the NMR structure can be influenced by the thermal
>> fluctuations in the backbone geometry.
>
> Well, that's part of it, but the way the models are derived contributes a lot.
>
>> Only in this respect the comparison of the two makes sense.
>> Is this correct?
>
> Comparisons can be made, but you have to formulate and justify your 
> assumptions.
>
> Cheers,
>
> Tsjerk
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
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Re: [gmx-users] rmsf question

[Andrei Neamtu]

Dear Mark and Tjerk,

Thank you for your comments.
If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
structure, is a measure of the uncertanty in resolving the structure.
Compared to this the RMSF of C-alpha computed from a MD trajectory
reflects the geometric fluctuations of the backbone in the Boltzmann
distribution of states in the generated ensemble.
The uncertanty in the NMR structure can be influenced by the thermal
fluctuations in the backbone geometry.
Only in this respect the comparison of the two makes sense.
Is this correct?

Many thanks again for your comments!

Andrei

On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham  wrote:
> On 15/03/2010 6:45 PM, Andrei Neamtu wrote:
>>
>> Dear Mark,
>>
>> Thank you very much for your response.
>>
>> What I meant was to obtain a RMSF plot form PDB mediated on each
>> residue and to compare with a RMSF plot mediated on each residue
>> obtained from a MD trajectory.
>> I do not compare a frame from PDB with a frame from MD trajectory.
>
> Sure. I didn't imply you needed or wanted to.
>
> g_rmsf -f your.pdb -s some_suitable.file -n some.ndx
> g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx
>
> In certain cases you'll get to use the same -s or -n, or have to juggle atom
> orders.
>
>> So, in the PDB file each 'frame' (MODEL) in the NMR file has the same
>> order and number of atoms.
>> This is also true for the MD trajectory.
>>
>> In the end i compare the two plots to see if the residues along the
>> chain have comparable 'flexibility'
>>
>> Is necessary in this case to have a correspondence between the order
>> of atoms in PDb and in MD trajectory?
>> In this sense the comparison makes sense? (I mean if I do the residue
>> mediation)
>
> You just need to make sure you are comparing equivalent things. If you just
> want (say) a C-alpha RMSF plot, then you can go ahead and do that if the
> index groups work. If you want all-atom RMSF then you might have some more
> fiddly work to do.
>
> Mark
>
>> (The PDB is a NMR structure and so it has the hydorgen added and no
>> missing side chains. And, it has the same number of atoms as the gro
>> file generated with pdb2gmx. And also the same number of atoms in the
>> corresponding residues.)
>>
>>
>>
>> Many thanks,
>> Andrei
>>
>>
>>
>> On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham
>>  wrote:
>>>
>>> On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
>>>>
>>>> Hi,
>>>>
>>>> is there a rapid way to compute RMSF on an NMR ensemble from a PDB file?
>>>
>>> Yes, but that's not your problem, it seems :-)
>>>
>>>> g_rmsf needs a .tpr file.
>>>
>>> Not true. Inspect the lines in g_rmsf -h describing the file types
>>> suitable
>>> for -f and -s. This is a fairly general GROMACS phenomenon.
>>>
>>>> This is OK with the MD trajectories but if I
>>>> want to compare MD ensemble one with the NMR RMSF ensemble
>>>> fluctuations from the original PDB this is not possible.
>>>
>>> That can be a trickier proposition. You need at least the atom order to
>>> correspond to make such a comparison.
>>>
>>> If the original atom names are suitable for defining the default groups,
>>> then you might be in business. Otherwise, you'll need to construct
>>> suitable
>>> input for -s (and maybe -n), and see if it matters whether different atom
>>> names in -f matter.
>>>
>>> Mark
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Re: [gmx-users] rmsf question

[Andrei Neamtu]

Dear Mark,

Thank you very much for your response.

What I meant was to obtain a RMSF plot form PDB mediated on each
residue and to compare with a RMSF plot mediated on each residue
obtained from a MD trajectory.
I do not compare a frame from PDB with a frame from MD trajectory.
So, in the PDB file each 'frame' (MODEL) in the NMR file has the same
order and number of atoms.
This is also true for the MD trajectory.

In the end i compare the two plots to see if the residues along the
chain have comparable 'flexibility'

Is necessary in this case to have a correspondence between the order
of atoms in PDb and in MD trajectory?
In this sense the comparison makes sense? (I mean if I do the residue mediation)

(The PDB is a NMR structure and so it has the hydorgen added and no
missing side chains. And, it has the same number of atoms as the gro
file generated with pdb2gmx. And also the same number of atoms in the
corresponding residues.)



Many thanks,
Andrei



On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham  wrote:
> On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
>>
>> Hi,
>>
>> is there a rapid way to compute RMSF on an NMR ensemble from a PDB file?
>
> Yes, but that's not your problem, it seems :-)
>
>> g_rmsf needs a .tpr file.
>
> Not true. Inspect the lines in g_rmsf -h describing the file types suitable
> for -f and -s. This is a fairly general GROMACS phenomenon.
>
>> This is OK with the MD trajectories but if I
>> want to compare MD ensemble one with the NMR RMSF ensemble
>> fluctuations from the original PDB this is not possible.
>
> That can be a trickier proposition. You need at least the atom order to
> correspond to make such a comparison.
>
> If the original atom names are suitable for defining the default groups,
> then you might be in business. Otherwise, you'll need to construct suitable
> input for -s (and maybe -n), and see if it matters whether different atom
> names in -f matter.
>
> Mark
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[gmx-users] rmsf question

[Andrei Neamtu]

Hi,

is there a rapid way to compute RMSF on an NMR ensemble from a PDB file?

g_rmsf needs a .tpr file. This is OK with the MD trajectories but if I
want to compare MD ensemble one with the NMR RMSF ensemble
fluctuations from the original PDB this is not possible.

Thanks,
Andrei
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[gmx-users] periodic moleules

[Andrei Neamtu]

Hi,

I am trying to build a hydrogel polymeric system and I want to make
use of the option periodic_molecules.
In this regard I am a little bit confused. are there any other
keywords except the option 'peridic molecules' that I have to set to
define a periodic polymer chain e.g. in the molecular topology file?
Because in the case  I define a bond between the last atom of the
chain and the first one, how does the grompp and mdrun know that the
molecule is periodic and not cyclic?

I also suppose that the angle and dihedrals that cross the periodic
border should also be defined.

Is there a place where I can find how to define periodic molecules in Gromacs?

Thanks a lot for any suggestions,

Andrei
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Re: [gmx-users] g_order warning message

[Andrei Neamtu]

Dear Justin,

thank you for your reply.

I am not trying to obtain the tethraedrality order parameter.
I want to use the g_order on a linear flexible molecule grafted to the
surface of the bilayer.
I think that the usual united atom order parameter (the component on
the direction perpendicular to the plane of the membrane) can give
information about the degree of alignment of this grafted linear
molecule (or an ensemble of molecules) with that axis. Do you think
this is correct?

How exactly is the g_order parameter calculated in Gromacs? I couldn't
find it in the manual.

Andrei

On Wed, Aug 5, 2009 at 1:43 PM, Justin A. Lemkul wrote:
>
>
> Andrei Neamtu wrote:
>>
>> Hello,
>>
>> I am trying to use g_order (gmx 4.0.5) on a coarse grained membrane.
>> Because the distances between two atoms two bonds apart is greater
>> than 0.3nm I keep receiving the message:
>>
>> .
>> Warming: distance between atoms * and X > 0.3 nm (**) .
>> Index file might be corrupt
>> Warming: distance between atoms * and X > 0.3 nm (**) .
>> Index file might be corrupt
>> Warming: distance between atoms * and X > 0.3 nm (**) .
>> Index file might be corrupt
>> Warming: distance between atoms * and X > 0.3 nm (**) .
>> Index file might be corrupt
>> Warming: distance between atoms * and X > 0.3 nm (**) .
>> Index file might be corrupt
>> . and so on
>>
>> I think that writing out these messages reduces the performance of the
>> g_order which takes a lot of time to complete.
>>
>> Does anyone know how to suppress these messages?
>>
>
> Not without changing the source code and re-compiling.  But is using g_order
> on a CG membrane appropriate?  The bond between the coarse particles doesn't
> even necessarily correspond to a C-C bond (or else you'd just be using a UA
> force field), so I would think that the reconstruction of tetrahedrality is
> not accurate.
>
> -Justin
>
>> Thank you,
>> Andrei
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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[gmx-users] g_order warning message

[Andrei Neamtu]

Hello,

I am trying to use g_order (gmx 4.0.5) on a coarse grained membrane.
Because the distances between two atoms two bonds apart is greater
than 0.3nm I keep receiving the message:

.
Warming: distance between atoms * and X > 0.3 nm (**) .
Index file might be corrupt
Warming: distance between atoms * and X > 0.3 nm (**) .
Index file might be corrupt
Warming: distance between atoms * and X > 0.3 nm (**) .
Index file might be corrupt
Warming: distance between atoms * and X > 0.3 nm (**) .
Index file might be corrupt
Warming: distance between atoms * and X > 0.3 nm (**) .
Index file might be corrupt
. and so on

I think that writing out these messages reduces the performance of the
g_order which takes a lot of time to complete.

Does anyone know how to suppress these messages?

Thank you,
Andrei
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[gmx-users] PME nodes

[Andrei Neamtu]

Hello,

How can I compile the g_tune_pme program available at:
http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/

Many thanks,
Andrei
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[gmx-users] pull code problem solved..

[Andrei Neamtu]

Sorry it appears that something was wrong with my .mdp file .. Idon't
know what ...but I wrote again the pull code lines and the warnings
dissapeared.

Thank you again,
Andrei
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[gmx-users] pull code problem

[Andrei Neamtu]

Hi Berk,
thank you for the reply

here is my mdp file:

;

;   User aneamtu

;   Joi, 7 mai - 2009

;   Input file

;

title  =  Production_runs

;define =  -DPOSRES -DPOSRES_CA2+_IONS



;constraints   =  all-bonds



integrator =  md

dt =  0.001 

nsteps =  5 



nstcomm=  1

nstxout=  1000

nstvout=  1000

nstfout=  1000

nstlog =  500
nstxtcout  =  50
xtc_grps   =  Protein_ions


nstenergy  =  100

nstlist=  10

ns_type=  grid


coulombtype=  PME

rlist  =  1.0

rcoulomb   =  1.0

rvdw   =  1.0
optimize_fft   =  yes


Tcoupl =  v-rescale

tc-grps=  Protein   SOL   ions

tau_t  =  0.1   0.1   0.1

ref_t  =  310   310   310



energygrps =  Protein  SOL CA2+ NA+ CL-



Pcoupl =  berendsen

Pcoupltype =  isotropic

tau_p  =  0.5

compressibility=  4.5e-5

ref_p  =  1.0



gen_vel=  no

gen_temp   =  310.0

gen_seed   =  173529



pull   =  constraint
pull_geometry  =  distance
pull_dim   =  Y Y Y
pull_nstxout   =  10
pull_nstfout   =  10
pull_ngroups   =  2
pull_group0=  Protein

pull_group1=  CA2+1
pull_rate1 =  0.3

pull_group2=  CA2+2
pull_rate2 =  0.3


I do not understand what I do wrong..
Should I use a -pi pull.ppa file like in gromacs 3.x ?

Andrei
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[gmx-users] pull code problem

[Andrei Neamtu]

hello,

I am trying to do a pulling simulation with gromacs 4.0.2

I added the following lines to the  .mdp input file for grompp:

...

pull   =  constraint
pull_geometry  =  distance
pull_dim   =  Y Y Y
pull_nstxout   =  10
pull_nstfout   =  10
pull_ngroups   =  2
pull_group0=  Protein

pull_group1=  CA2+1
pull_rate1 =  0.3

pull_group2=  CA2+2
pull_rate2 =  0.3

.

when I run
> grompp -f production_prm.mdp ...etc.

it does not recognize the keywords for pulling:

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to
./#neutr_RCK_Mthk_solv.04.mdout.mdp.6#

WARNING 1 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_geometry' in parameter file

WARNING 2 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_dim' in parameter file

WARNING 3 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_nstxout' in parameter file

WARNING 4 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_nstfout' in parameter file

WARNING 5 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_ngroups' in parameter file

WARNING 6 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group0' in parameter file

WARNING 7 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group1' in parameter file

WARNING 8 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_rate1' in parameter file

WARNING 9 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group2' in parameter file

WARNING 10 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_rate2' in parameter file

...

It appears that grompp doesnot recognize any of these keywords...

Does anybody can help?

Thank you
Andrei
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[gmx-users] Re: Martini Cg-model can not be downloaded!

[Andrei Neamtu]

Which browser do you us? I had the same problem with Internet
explorer. Try Firefox!
Andrei
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Re: [gmx-users] Martini Cg-model can not be downloaded!

[Andrei Neamtu]

I had the same problem with Internet explorer. Try Firefox!
Andrei

On Tue, Feb 10, 2009 at 9:41 AM, xi zhao  wrote:
> well.. it seems that there is a problem in the page for downloading files
> from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model
> parameters can not be downloaded!
> Thank you for help!
>
>
>
> 
> 好玩贺卡等你发，邮箱贺卡全新上线！
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Re: [gmx-users] PBC only in xy direction

[Andrei Neamtu]

Hi,

How is it possible a vacuum layer be maintained without solvent
evaporation? (in absence of few solvent layers positionally restrained
or in absence of walls which work only in pbc=xy)

Andrei
(maybe the question is trivial but I cannot figure out the answer)


On Thu, Dec 11, 2008 at 11:50 AM, Berk Hess <[EMAIL PROTECTED]> wrote:
> Hi,
>
> This is not possible in 3.3.
>
> But in practice you almost never need this,
> since it is far more efficient to use pbc=xyz and have a slab of vacuum
> in between the periodic images in z.
>
> Berk
>
>> Date: Thu, 11 Dec 2008 10:30:55 +0100
>> From: [EMAIL PROTECTED]
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] PBC only in xy direction
>>
>> Hi gmx-users,
>>
>> We are using the version 3.3.3. Is there also a posibility to have pbc
>> only in xy direction (as I saw it is possible in Gromacs 4.0)? The
>> manual says nothing about that.
>>
>> Thank you in advance.
>>
>> Best regards,
>> Andrea
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> 
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Re: [gmx-users] error while compiling gromacs 4.0.2

[Andrei Neamtu]

try to add in your .bashrc this

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi-1.2.8/lib

or whatever your mpi lib directory is

Andrei


On Thu, Dec 4, 2008 at 12:08 PM, Ragothaman Yennamalli
<[EMAIL PROTECTED]> wrote:
> Dear all,
> While compiling gromacs 4.0.2 in a AMD 64bit dual processor system, I 
> encounter the following error while configuring:
>
> checking size of int... configure: error: cannot compute sizeof (int)
> See `config.log' for more details.
>
> Please let me know where I have gone wrong. I am pasting the entire messages 
> below:
>
>
> [EMAIL PROTECTED] gromacs-4.0.2]$ ./configure --enable-mpi --enable-float
> 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 catamount... no
> checking how to run the C preprocessor... mpicc -E
> checking whether mpicc accepts -O3... yes
> checking whether mpicc accepts -funroll-all-loops... yes
> checking whether mpicc accepts  -O3 -fomit-frame-pointer -finline-functions 
> -Wall -Wno-unused -funroll-all-loops... yes
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... no
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking whether byte ordering is bigendian... no
> checking for int... yes
> checking size of int... configure: error: cannot compute sizeof (int)
> See `config.log' for more details.
>
>
> Thanks in advance,
>
> With Kind Regards,
>
> Ragothaman
>
>
>  Add more friends to your messenger and enjoy! Go to 
> http://messenger.yahoo.com/invite/
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[gmx-users] test particle insertion

[Andrei Neamtu]

Hello,

Where can be found more information on test particle insertion method
as implemented in gromacs? It is possible to use molecules as test
particles?

Thank you a lot,
Andrei
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Re: [gmx-users] problem with npt

[Andrei Neamtu]

Hi,
have you checked if there is no water inside the membrane after the
use of genbox?

On Dec 16, 2007 1:35 PM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> pragya chohan wrote:
> >
> > i started with the lipid coordinates from peter tieleman and removed the
> > water. then i added water by genbox.
> > I did energy minimization followed by position restrain, which I removed
> > gradually. all of it was done under npt. I carried out npt for 250
> > ps. During the next 250 ps npt run the bilayers separated and deformed.
>
> Usually NVT to get the temperature right before relaxing to NPT to let
> the density equilibrate can be good idea. Look at how much your box
> changed size during your NPT to see if this effect is causing problems.
>
>
> Mark
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[gmx-users] make hole question

[Andrei Neamtu]

Hello gmx,

I have a quick question:

with what distribution of gromacs the mdrun make hole works?

Cu bine,
Andrei
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[gmx-users] infiniband question

[Andrei Neamtu]

Hello gmx,

I have a question regarding infiniband interconnect: Is
there any difference (in terms of performance) between integrated
on-board infiniband (ex. Mellanox) and PCI-Express infiniband adaptors
(due to pci-e limitations)? Which one is recomended. We are in a
process of buying a cluster on which gromacs will be the main
computational engine.
Any help will be greatly appreciated!
Thank you,
Andrei
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[gmx-users] re:multi problem

[Andrei Neamtu]

Thanks a lot Mark and Ye, I will try both alternatives!

Andrei


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[gmx-users] re:multi problem again

[Andrei Neamtu]

Dear Mark,

Thank you for your reply!

I thought that maybe the accessibility were the problem. I don't  
figure how to set the working directory of say node 1 to my current  
working directory on node 0.
I setup node 1 to be able to access node 0 through ssh with no  
password but the problem remains. So .. I'm stuck here.
Any idea where to start digging solving the most probable  
accessibility problem?


In short there is how I made the GROMACS installation:

1. I installed GROMACS (serial and parallel version) on every node
2. I setup the node 0 to be able to access all other nodes through ssh  
without password

3. generated on node 0 the nodesfile file for lam booting

I must say that parallel simulations run fine on the entire cluster (I  
mean a single system split on all nodes). The only problem appears  
when I try using -multi to simulate several copies of the system along  
the nodes.


Do I have to use a file sharing system or something like this ...?
It is the first time I try to use the -multi option.

Thank you a lot,
Andrei


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[gmx-users] multi problem

[Andrei Neamtu]

Dear gmx users,

I have problems in running a simulation on several nodes using the  
-multi option:


I make the .tpr files for different temperatures (I want to use the REMD code)


grompp -f param0.mdp -po param0.out.mdp -c conf.gro -p topol.top -o sim0.tpr
grompp -f param1.mdp -po param1.out.mdp -c conf.gro -p topol.top -o sim1.tpr
grompp -f param2.mdp -po param2.out.mdp -c conf.gro -p topol.top -o sim2.tpr
.
.
.
grompp -f paramN.mdp -po paramN.out.mdp -c conf.gro -p topol.top -o simN.tpr

where N is the number of nodes in my cluster (P4 with gigabit ethernet)

After the collection of input .tpr files are generated I start the  
simulations with:


mpirun -np N mdrun_mpi -np N -multi -replex 2000 -s sim.tpr -o sim.trr ...

but the program stops saying that it cannot find the sim1.tpr, sim2.tpr 
It do *FINDS* the sim0.tpr for the node where I start the simulation  
but for the rest of nodes it doesn't.


I tried to put the simulation on a multi core machine (2 cores) and it  
works fine for N=2. But when I link 2 multicore machines the program  
stops with the same message except that the first .tpr file not found  
is the one corresponding to the second machine.


I saw on the list that there were similar problems in the past but I  
didn't find any solution to them. I tried to soft link the mdrun_mpi  
executable in the working directory but the problem persists.


Any help to solve this problem?


Thanks a lot,
Andrei





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[gmx-users] performance question

[Andrei Neamtu]

Hello,

We are in the process of building a cluster on which GROMACS will be  
the main computational engine and I have a question about performance.  
We are not yet decided what to buy (we can not test them in advance).


Which configuration do you think will be better:
- 8 servers with 2 x dual core opterons 2220 (2,8 GHz) = 32 cores
or
- 4 servers with 2 x quad core Xeons 5335 (2.0 GHz) = 32 cores

Both configurations with Infiniband Interconnect. My opinion is that  
the  Xeon based should be the choice because of its 128 sse bus, but I  
don't know what to say about the clock speed difference.


Thank you,
Andrei


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