Re: [gmx-users] Re: g_hbond output

[Jianguo Li]

If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff 
distance and the cutoff angle. $3 is the number of pairs within the cutoff 
distance, but beyond the cutoff angle. You may got different number of hbonds 
using different cutoff distance and cutoff angle.
Jianguo




From: ZHAO Lina 
To: Discussion list for GROMACS users 
Sent: Wednesday, 16 March 2011 13:33:57
Subject: [gmx-users] Re: g_hbond output

@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 0   0   0
   200   0   0
   400   2   1
   600   0   3
   800   0   2
  1000   1   0
:
 5   3   2

Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the 
$3 
means pairs.

I tried pymol, and on the last frame,
there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2

Thanks and sorry for last email without my realization it sent.

lina


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Re: [gmx-users] Re: g_hbond output

[ZHAO Lina]

 s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 0   0   0
   200   0   0
   400   2   1
   600   0   3
   800   0   2
  1000   1   0

Here is my question, since there is already one bond formed, then why there
is none pairs in 1000?


On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li  wrote:

> If I understand correctly, $2 is the number of hydrogen bonds defined by
> cutoff distance and the cutoff angle. $3 is the number of pairs within the
> cutoff distance, but beyond the cutoff angle. You may got different number
> of hbonds using different cutoff distance and cutoff angle.
> Jianguo
>
> --
> *From:* ZHAO Lina 
> *To:* Discussion list for GROMACS users 
> *Sent:* Wednesday, 16 March 2011 13:33:57
> *Subject:* [gmx-users] Re: g_hbond output
>
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>  0   0   0
>200   0   0
>400   2   1
>600   0   3
>800   0   2
>   1000   1   0
> :
>  5   3   2
>
> Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if
> the $3 means pairs.
>
> I tried pymol, and on the last frame,
> there were 4 hydrogen bonds, between 7 residues. it's different from here 3
> 2
>
> Thanks and sorry for last email without my realization it sent.
>
> lina
>
>
> --
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Re: [gmx-users] Energy calculation

[C.Y. Chang]

Hi,

I try to calculate the Hbond in the ligand and remove the duplicate atoms in
the .ndx file dumped from g_hbond.
This is the contents in the .ndx file.

[ HBD ]
 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530
[ HBA ]
 17367  17375  17381  17384  17387  17388  17400  17404  17412  17418
17421  17424  17425  17437  17441
 17449  17455  17458  17461  17462  17474  17478  17486  17492  17495
17498  17499  17511  17515  17523
 17529  17532  17535  17536  17548

And then, I perfrom the grompp.
It shows the error msg.

Fatal error:
atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in
different energy groups

How should I deal with the problem?



On the other side, I read the information in the web page (
http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html)
I remove the lines in the [bonds] region in .top files.
But I still get these terms

  1  Angle2  G96Angle 3  Proper-Dih.  4
Ryckaert-Bell.
  5  Improper-Dih.6  LJ-147  Coulomb-14   8  LJ-(SR)
  9  Disper.-corr.   10  Coulomb-(SR)11  Coul.-recip.12
Position-Rest.
 13  Potential   14  Kinetic-En. 15  Total-Energy16  Temperature
 17  Pres.-DC18  Pressure19  Constr.-rmsd20  Box-X
 21  Box-Y   22  Box-Z   23  Volume  24  Density
 25  pV  26  Enthalpy27  Vir-XX  28  Vir-XY
 29  Vir-XZ  30  Vir-YX  31  Vir-YY  32  Vir-YZ
 33  Vir-ZX  34  Vir-ZY  35  Vir-ZZ  36  Pres-XX
 37  Pres-XY 38  Pres-XZ 39  Pres-YX 40  Pres-YY
 41  Pres-YZ 42  Pres-ZX 43  Pres-ZY 44  Pres-ZZ
 45  #Surf*SurfTen   46  Mu-X47  Mu-Y48  Mu-Z
 49  Coul-SR:LIG-LIG 50  LJ-SR:LIG-LIG
 51  Coul-14:LIG-LIG 52  LJ-14:LIG-LIG
 53  Coul-SR:LIG-DPPC_SOL54  LJ-SR:LIG-DPPC_SOL
 55  Coul-14:LIG-DPPC_SOL56  LJ-14:LIG-DPPC_SOL
 57  Coul-SR:DPPC_SOL-DPPC_SOL   58  LJ-SR:DPPC_SOL-DPPC_SOL
 59  Coul-14:DPPC_SOL-DPPC_SOL   60  LJ-14:DPPC_SOL-DPPC_SOL
 61  T-DPPC  62  T-SOL   63  T-LIG   64  Lamb-DPPC
 65  Lamb-SOL66  Lamb-LIG

And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ],
but it is the same.
Where is the wrong process? And how could I get the angle and dihedral
energy in the intramolecules?
Thanks for your any comments.
Best,

Chia-yun


2011/3/14 Mark Abraham 

>
>
> On 14/03/11, *"C.Y. Chang" *  wrote:
>
> Hi,
>
> I try to calculate hydrogen bond (HB) energy.
> The g_energy does not have this term.
> And I find the g_hbond function in Gromacs.
> But the HB energy calculation is not in g_hbond.
>
>
> There's good reasons for this. How would you define the "HB energy" in
> terms of the kind of information accessible to MD simulations?
>
>
> Therfore, I also try to dump the .ndx file including the HB_donor,
> HB_acceptor and HB_system from g_hbond, and perfrom the grompp
> But there is a error msg,
>
> Atom 17380 in multiple Energy Mon. groups
>
>
> Look up energy groups in the manual - start of section 3.3. Your .mdp file
> is defining an illegal combination of atoms and energy monitor groups.
>
>
> Another problem is about calculating the intramolecular energy e.g.
> 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid
> layer-ligand complex system.
> I could set up the energy_grp and calculate energy between the ligand group
> and the lipid layer group.
> But I need the intramolecular energy in the groups.
> How should I deal with these problems?
>
>
> An inter-group energy doesn't mean anything much, so don't bother. Please
> read the whole of this thread
> http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Energy calculation

[Mark Abraham]

On 16/03/11, "C.Y. Chang"   wrote:
> Hi, 
> 
> I try to calculate the Hbond in the ligand and remove the duplicate atoms in 
> the .ndx file dumped from g_hbond.
> This is the contents in the .ndx file.
> 
> [ HBD ]
>  17385 17382 17422 17419 17459 17456 17496 17493 17533 17530
> 
> [ HBA ]
>  17367  17375  17381  17384  17387  17388  17400  17404  17412  17418  17421  
> 17424  17425  17437  17441
>  17449  17455  17458  17461  17462  17474  17478  17486  17492  17495  17498  
> 17499  17511  17515  17523
> 
>  17529  17532  17535  17536  17548
> 
> And then, I perfrom the grompp.
> It shows the error msg.
> 
> Fatal error:
> atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in 
> different energy groups
> 
> 
> How should I deal with the problem?
> 

Redefine charge or energy groups as appropriate for whatever you're trying to 
do. Non-bonded interactions are calculated by looping over atom-atom 
interactions grouped by charge group and then by energy group. Every charge 
group must be a subset of an energy group or fully disjoint from it.


> On the other side, I read the information in the web page 
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html)
> 
> I remove the lines in the [bonds] region in .top files.
> But I still get these terms
> 
>   1  Angle    2  G96Angle 3  Proper-Dih.  4  
> Ryckaert-Bell.
>   5  Improper-Dih.    6  LJ-14    7  Coulomb-14   8  LJ-(SR)
> 
>   9  Disper.-corr.   10  Coulomb-(SR)    11  Coul.-recip.    12  
> Position-Rest.
>  13  Potential   14  Kinetic-En. 15  Total-Energy    16  Temperature
>  17  Pres.-DC    18  Pressure    19  Constr.-rmsd    20  Box-X
> 
>  21  Box-Y   22  Box-Z   23  Volume  24  Density
>  25  pV  26  Enthalpy    27  Vir-XX  28  Vir-XY
>  29  Vir-XZ  30  Vir-YX  31  Vir-YY  32  Vir-YZ
> 
>  33  Vir-ZX  34  Vir-ZY  35  Vir-ZZ  36  Pres-XX
>  37  Pres-XY 38  Pres-XZ 39  Pres-YX 40  Pres-YY
>  41  Pres-YZ 42  Pres-ZX 43  Pres-ZY 44  Pres-ZZ
> 
>  45  #Surf*SurfTen   46  Mu-X    47  Mu-Y    48  Mu-Z
>  49  Coul-SR:LIG-LIG 50  LJ-SR:LIG-LIG
>  51  Coul-14:LIG-LIG 52  LJ-14:LIG-LIG
>  53  Coul-SR:LIG-DPPC_SOL    54  LJ-SR:LIG-DPPC_SOL
> 
>  55  Coul-14:LIG-DPPC_SOL    56  LJ-14:LIG-DPPC_SOL
>  57  Coul-SR:DPPC_SOL-DPPC_SOL   58  LJ-SR:DPPC_SOL-DPPC_SOL
>  59  Coul-14:DPPC_SOL-DPPC_SOL   60  LJ-14:DPPC_SOL-DPPC_SOL
>  61  T-DPPC  62  T-SOL   63  T-LIG   64  Lamb-DPPC
> 
>  65  Lamb-SOL    66  Lamb-LIG
> 
> And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], 
> but it is the same.
> Where is the wrong process? And how could I get the angle and dihedral energy 
> in the intramolecules?
> 
> Thanks for your any comments.
> 

You're decomposing PME electrostatics. That produces garbage values for 
quantities that have little meaning, like it says in the thread I suggested you 
read the whole of. I'm going to stop helping :-)

Mark


> 
> Best,
> 
>     Chia-yun
> 
> 
> 2011/3/14 Mark Abraham 
> 
> 
> > 
> > 
> > On 14/03/11, "C.Y. Chang"   wrote:
> > > 
> > > Hi,
> > > 
> > > I try to calculate hydrogen bond (HB) energy.
> > > The g_energy does not have this term.
> > > And I find the g_hbond function in Gromacs.
> > > But the HB energy calculation is not in g_hbond.
> > > 
> > 
> > 
> > 
> > There's good reasons for this. How would you define the "HB energy" in 
> > terms of the kind of information accessible to MD simulations?
> > 
> > 
> > > 
> > > Therfore, I also try to dump the .ndx file including the HB_donor, 
> > > HB_acceptor and HB_system from g_hbond, and perfrom the grompp
> > > 
> > > But there is a error msg,
> > > 
> > > Atom 17380 in multiple Energy Mon. groups
> > > 
> > 
> > 
> > Look up energy groups in the manual - start of section 3.3. Your .mdp file 
> > is defining an illegal combination of atoms and energy monitor groups.
> > 
> > 
> > 
> > > Another problem is about calculating the intramolecular energy e.g. 
> > > 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid 
> > > layer-ligand complex system.
> > > 
> > > 
> > > I could set up the energy_grp and calculate energy between the ligand 
> > > group and the lipid layer group.
> > > But I need the intramolecular energy in the groups.
> > > How should I deal with these problems?
> > > 
> > 
> > 
> > 
> > An inter-group energy doesn't mean anything much, so don't bother. Please 
> > read the whole of this thread 
> > http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html
> > 
> > 
> > Mark
> > 
> > --
> > 
> > gmx-users mailing list    gmx-users@gromacs.org
> > 
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > 
>

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 106

[sa]

Thank you Angel, I will try your suggestion.

Cheers

SA

>
>
>
> Hi
> very recently I faced the same problem with a system that gives micelles
> of different geometries and, as far as I saw, g_order don't do that.
> Then I decided to compute a kind of local order parameters defined as:
>
> S_i=(3 cos(\theta)-1)/2
>
> where theta is the angle between the segments joining the carbon atoms
> (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find this
> reasonable for your analysis...
>
> Cheers,
>
> Ángel.
>
>
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Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106

[Ángel Piñeiro]

Then, please, let us know how it works for your systems. The results for
my systems were exactly as expected. This allows to evaluate the order
of the C-chains regardless their orientation... but I do not know if
there is a better method to do this. I would be happy to know the
opinion of anyone else who want to try this or to propose an alternative
method.

Cheers,

Ángel.



On Wed, 2011-03-16 at 09:42 +0100, sa wrote:

> Thank you Angel, I will try your suggestion.
> 
> Cheers
> 
> SA
> 
> 
> 
> 
> Hi
> very recently I faced the same problem with a system that
> gives micelles
> of different geometries and, as far as I saw, g_order don't do
> that.
> Then I decided to compute a kind of local order parameters
> defined as:
> 
> S_i=(3 cos(\theta)-1)/2
> 
> where theta is the angle between the segments joining the
> carbon atoms
> (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find
> this
> reasonable for your analysis...
> 
> Cheers,
> 
> Ángel.
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: g_hbond output

[Jianguo Li]

A pair within the cutoff distance (e.g., 0.35nm) either belongs to $2 or $3, 
but 
cannot belong to both columns. 

If the program finds a pair shorter than 0.35nm, and the angle is smaller than 
30deg., then the program put this pair in the column 2.
If the program finds a pair shorter than 0.35nm, and the angle is larger than 
30deg., then the program put this pair in the column 3.

Jianguo





From: ZHAO Lina 
To: Discussion list for GROMACS users 
Sent: Wednesday, 16 March 2011 15:31:30
Subject: Re: [gmx-users] Re: g_hbond output

  
 
 
 
 
 s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 0   0   0
   200   0   0
   400   2   1
   600   0   3
   800   0   2
  1000   1   0

Here is my question, since there is already one bond formed, then why there is 
none pairs in 1000?



On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li  wrote:

If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff 
distance and the cutoff angle. $3 is the number of pairs within the cutoff 
distance, but beyond the cutoff angle. You may got different number of hbonds 
using different cutoff distance and cutoff angle.
>Jianguo
>
>
>

From: ZHAO Lina 
>To: Discussion list for GROMACS users 
>Sent: Wednesday, 16 March 2011  13:33:57
>Subject: [gmx-users] Re: g_hbond output
>
>
>@ legend length 2
>@ s0 legend "Hydrogen bonds"
>@ s1 legend "Pairs within 0.35 nm"
> 0   0   0
>   200   0   0
>   400   2   1
>   600   0   3
>   800   0   2
>  1000   1   0
>:
> 5   3   2
>
>Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the 
>$3 
>means pairs.
>
>I tried pymol, and on the last frame,
>there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2
>
>Thanks and sorry for last email without my realization it sent.
>
>lina
>
>
>--
>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!
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>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>


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Re: [gmx-users] Pulling

[mohsen ramezanpour]

Dear Chris
Thanks for your reply

2-When you limit your sampling phase space,it can make some Errors,Because
you may ignore
some important regions(where you don't know them and you can't predict
there).
In the other hands,When we pull drug along a line,although we had not
restrain it, but in fact they are equivalent!
Because the orientation of drug dosen't change during the simulation(Because
doing umberella sampling dosen't change the orientation too).
Is it possible to do Umbrella Sampling while the drug be free to rotate
along with oscilation in windows?

On Tue, Mar 15, 2011 at 9:49 AM,  wrote:

> 1. yes. it is acceptable. It is different, but neither method is de facto
> better.
>
> 2. to enhance convergence by limiting the amount of phase space that must
> be sampled. Changing the restraints can change the profile, but if you care
> only about the integrated standard binding free energy then it does not
> change the converged result. See, for example, D. L. Mobley, J. D. Chodera,
> K. A. Dill. "On the use of orientational restraints and symmetry number
> corrections in alchemical free energy calculations", ...
>
> Chris.
>
> -- original message --
>
> Dear All
> Afew question about Pulling in Umberella Sampling
>
> 1-the goal of pulling is making some primary structures (in different
> distances) to do umberella sampling for each one of them.
>  I can make these states by transporting my ligands along a vector to
> prepare these primary structures.Is this correct?Now I can do US for each
> one!without any need to doing pulling.
>
> 2-Why do we keep fix the relative orientation of Protein-ligand during the
> pulling ? I think changing the orientation of ligand during the
> pulling(suppose the protein is restrain) can chang our result?
>  Because our umbrella sampling maintain this orientation too.am I right?
>
> Thanks in advance
> -- next part --
>
>
> --
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Re: [gmx-users] Umberella sampling

[mohsen ramezanpour]

Dear chris
Thanks for your reply

1-I am not sure,Since we need the know the variations of free energy along a
specific degree of freedom of system(for example z axis),so  the springs
must be 1 dimensional to allow drug to oscilate only in one dimension(z
axis).
Let me say my question in other words:
Do we need to do sampling just in phase space related to z axis(1
dimensional) or we can do sampling in other places(if it be 3
dimensional),Although we still want the variation of free energy along z
axis?

2-evry windows have a width(for example 0.02 nm),Besides according to Hock's
law knowing the oscilation amplitude is possible when you have the K and the
mass and total energy:1/2 k(x/2)^2=1/2 m v(max)^2

3-my question in other words:
Since we need overlapping the distribution densities of each windows,Does
the drug need to enter to the neighbour windows a little ?
Thanks in advance for your reply
On Tue, Mar 15, 2011 at 9:54 AM,  wrote:

> 1. Depends on how you set them in your .mdp file. It could be either.
>
> 2. There is no general method. Use trial and error. Also, your question is
> flawed, K defines X. Unless by "length of one windows" you meant the
> distance between neighbouring centers of restraint (umbrellas).
>
> 3. you need overlapping distributions. Let's leave it at that. I have not
> seen any general treatment of what K is required and I am rather sure that
> it is impossible to predetermine the necessary force constants (K) unless
> you know the PMF. If you need to know the PMF beforehand then this is not a
> general solution and also probably useless since the whole purpose is to get
> the PMF.
>
> Chris.
>
> -- original message --
>
> Dear All
> afew question in umberella sampling tutorial:
> 1-We do umberella sampling for each of 25 simulation windows,while using a
> spring(harmonic potential),Are these springs 1 or 3 dimensional?
>
> 2-Suppose the length of one windows is X nm,what is the  approperiate K
> (spring constant) for this window?Is there a general way to determine this
> value?
>
> 3-I think the K must be such that the oscilation amplitude be  a few larger
> than X/2, because we need overlapping of density distribution for analysing
> with wham method, am I right?
>
> Thanks in advance
>
>
>
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[gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ?

[maria goranovic]

Hello

I am trying to pdb2gmx with a free amino acid in amber99sb as follows:

pdb2gmx -f temp.pdb -ff amber99sb

there are no ter records in the input pdb file.

However, pdb2gmx fails with the following error:

---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2gmx.c, line: 284

Fatal error:
In the chosen force field there is no residue type for 'GLU' as a starting
terminus
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Is this some kind of bug. If so, is there a workaround? For example, can I
have the amino acid bound to the terminus of the larger protein (for which
the free amino acid is a ligand) and make the bond have a zero spring
constant or something?

Maria


Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ?

[David van der Spoel]

On 2011-03-16 11.29, maria goranovic wrote:

Hello

I am trying to pdb2gmx with a free amino acid in amber99sb as follows:

pdb2gmx -f temp.pdb -ff amber99sb

there are no ter records in the input pdb file.

However, pdb2gmx fails with the following error:

---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2gmx.c, line: 284

Fatal error:
In the chosen force field there is no residue type for 'GLU' as a
starting terminus
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Is this some kind of bug. If so, is there a workaround? For example, can
I have the amino acid bound to the terminus of the larger protein (for
which the free amino acid is a ligand) and make the bond have a zero
spring constant or something?


This is a missing feature in the FF. Since charges are different for 
N-terminal and C-terminal residues in Amber there are separate 
N-terminal and C-terminal variants of (almost) all residues, but not for 
isolated AA. Your best bet is to use Antechamber to make a GAFF 
topology which you can convert to gromacs again.


Maria


Maria G.
Technical University of Denmark
Copenhagen




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[gmx-users] installation of gromacs

[Thomas Koller]

Hello,

I did the procedure as described, but at the end of the configuration of 
gromacs, I obtain this message:

checking size of void*... configure: error: cannot compute sizeof (void*)
See `config.log' for more details.

What is the problem?

Regards,
Thomas
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Re: [gmx-users] installation of gromacs

[Mark Abraham]

On 16/03/11, Thomas Koller   wrote:
> Hello,
> 
> I did the procedure as described, but at the end of the configuration of 
> gromacs, I obtain this message:
> 
> checking size of void*... configure: error: cannot compute sizeof (void*)
> See `config.log' for more details.
> 
> What is the problem?
> 

Many possibilities exist. Unfortunately, we don't know anything about your 
intentions, configure command, system environment or the contents of config.log 
a few hundred lines from the end where it noticed the error.

Mark
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[gmx-users] Fwd: membrane protein

[mohsen ramezanpour]

-- Forwarded message --
From: mohsen ramezanpour 
Date: Wed, Mar 9, 2011 at 2:49 PM
Subject: membrane protein
To: Discussion list for GROMACS users 


Dear All

in membrane protein tutorial:

What is the P-N vector?

RMSD for what group do I need to calculate?

How can I estimate the helix tilt?

Thanks in advance
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[gmx-users] Fwd: membrane-protein

[mohsen ramezanpour]

-- Forwarded message --
From: mohsen ramezanpour 
Date: Tue, Mar 8, 2011 at 11:33 PM
Subject: membrane-protein
To: Discussion list for GROMACS users 


Dear All

doing membrane protein tutorial of Dr.Justin I have a few question,

1-Why do I need to know the stabilization state of my box vector?

2-How can I do this (with wich program?)?

3-What can I do if they were not stable?

Thanks in advance
Mohsen
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[gmx-users] Phd positions in SISSA

[Giovanni Bussi]

Dear all,

since many people in our group are gromacs users, this announcement
could make some sense on the gmx mailing list. Please forward it to
interested people.

Best wishes,

Giovanni Bussi

#

Job Description: Applicants should have a good background in Physics,
Chemistry or related subjects and are expected to obtain their Laurea
Specialistica or equivalent degree by Autumn 2011.

Applicants will be first screened based on their CV (educational track
record, letters of presentation, preprints or publications). Those
that pass the preliminary screening will be invited to participate to
the local selection taking place around mid April 2011.

Admitted students will have the opportunity to follow a one-year
educational program in an international and interdisciplinary
environment, followed by two or three years of active research in one
of the following areas:

* structural bioinformatics,
* statistical mechanics of complex molecular systems,
* biomolecular simulations,
* simulations of rare events.

For further information about the available research lines, and past
entrance exams see the Statistical and Biological Physics Sector
website (www.sissa.it/sbp)

To apply:
The application should be filled exclusively online at the following
address: www.sissa.it/applications/phd . The application deadline is
March 31st.
Notice that SISSA can cover, in full or in part, the expenses of
students who are admitted to the local entrance exam. Please contact
p...@sissa.it for further information.

About SISSA:
The International School for Advanced Studies of Trieste. SISSA was
the first Italian university to offer the PhD degree, and has
continued to do so with notable success. Since its founding in 1978,
SISSA has prepared more than 500 young people for careers in research
and teaching.

According to a recent independent comprehensive academic survey SISSA
is the leading Italian university in terms of density of top
scientists. In the latest evaluation of the Italian university system
(CIVR) it was judged as the most exciting of the small research
centers in Italy in physics and mathematics and came second in
biology.

Facilities:
People who study at SISSA, which is situated in the campus in Via
Bonomea in a park of over 100,000 m2, have access to an excellent
library which is open 24 hours a day; they have a computer at their
disposal with which to connect to the huge resources for scientific
computing and internet services; they receive support in finding
accommodation in the city from the housing service and a monthly
contribution from the School towards the rent; on the campus they can
find a restaurant, kindergarten, and meditation and music rooms.
Students from non-European Union countries have their enrolment in the
Italian national health service reimbursed. Female students receive a
contribution during their maternity leave. Students are awarded
scholarships for the entire duration of their training programmes.

Start date: November 2011. Earlier starts are possible through
pre-doctoral scholarships.

Duration: 3 to 5 years

Funding Source: MIUR

Salary on grant: SISSA tops the Ministerial doctoral salaries with an
additional financial contribution and provides benefits such as
partial support of house rent, laptop equipment etc. Please contact
p...@sissa.it to enquire about the current exact amount of the various
financial aspects

Contact Person (Referent): Cristian Micheletti

Ref. E-Mail: miche...@sissa.it

Group Web Page: http://www.sissa.it/sbp
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[gmx-users] g_order for DPC alkyl chain in the micelle

[sa]

Hi all

This message is related with my previous message (see below) about the
calculation of the order value for the DPC alkyl chain in a micelle. So if I
understand well the previous angel's message, I need to compute the theta
angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2). So for
carbon atom C14, I have created an index file with two groups defined as
following

aC14 | aC16  and aC14 | aC16 with make_ndx_mpi

and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 10 -e 101000
-n index.ndx and choose the C13_C15 and C14_C16 groups. Unfortunately i
obtain the following error

Group C13_C15 contains the following atoms:
Atomname 0: C13
Atomname 1: C15
Atomname 2: C13
Atomname 3: C15
Atomname 4: C13
Atomname 5: C15
Atomname 6: C13
Atomname 7: C15
Atomname 8: C13
Atomname 9: C1
...

Group C14_C16 contains the following atoms:
Atomname 0: C14
Atomname 1: C16
Atomname 2: C14
Atomname 3: C16
Atomname 4: C14

...
Atomname 105: C16
Atomname 106: C14
Atomname 107: C16

Careful: distance only makes sense in some situations.

Reading frame   0 time 10.000
Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#

---
Program g_sgangle_mpi, VERSION 4.5.3
Source code file: gmx_sgangle.c, line: 127

Fatal error:
Something wrong with contents of index file.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Did I make a error, what is the correct approach. to obtain the angle
between 2 vectors ?

Thank you in advance

SA



> --
>
> Message: 3
> Date: Wed, 16 Mar 2011 10:06:44 +0100
> From: ?ngel Pi?eiro 
> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
> To: Discussion list for GROMACS users 
> Message-ID: <1300266404.6843.29.camel@arginine>
> Content-Type: text/plain; charset="utf-8"
>
> Then, please, let us know how it works for your systems. The results for
> my systems were exactly as expected. This allows to evaluate the order
> of the C-chains regardless their orientation... but I do not know if
> there is a better method to do this. I would be happy to know the
> opinion of anyone else who want to try this or to propose an alternative
> method.
>
> Cheers,
>
> Ã ngel.
>
>
>
> On Wed, 2011-03-16 at 09:42 +0100, sa wrote:
>
> > Thank you Angel, I will try your suggestion.
> >
> > Cheers
> >
> > SA
> >
> >
> >
> >
> > Hi
> > very recently I faced the same problem with a system that
> > gives micelles
> > of different geometries and, as far as I saw, g_order don't do
> > that.
> > Then I decided to compute a kind of local order parameters
> > defined as:
> >
> > S_i=(3 cos(\theta)-1)/2
> >
> > where theta is the angle between the segments joining the
> > carbon atoms
> > (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find
> > this
> > reasonable for your analysis...
> >
> > Cheers,
> >
> > Ã ngel.
> >
> >
>
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Re: [gmx-users] g_order for DPC alkyl chain in the micelle

[Justin A. Lemkul]

sa wrote:

Hi all

This message is related with my previous message (see below) about the 
calculation of the order value for the DPC alkyl chain in a micelle. So 
if I understand well the previous angel's message, I need to compute the 
theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2). 
So for carbon atom C14, I have created an index file with two groups 
defined as following


aC14 | aC16  and aC14 | aC16 with make_ndx_mpi

and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 10 -e 
101000 -n index.ndx and choose the C13_C15 and C14_C16 groups. 
Unfortunately i obtain the following error


Group C13_C15 contains the following atoms:
Atomname 0: C13
Atomname 1: C15
Atomname 2: C13
Atomname 3: C15
Atomname 4: C13
Atomname 5: C15
Atomname 6: C13
Atomname 7: C15
Atomname 8: C13
Atomname 9: C1
...

Group C14_C16 contains the following atoms:
Atomname 0: C14
Atomname 1: C16
Atomname 2: C14
Atomname 3: C16
Atomname 4: C14

...
Atomname 105: C16
Atomname 106: C14
Atomname 107: C16

Careful: distance only makes sense in some situations.

Reading frame   0 time 10.000
Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#

---
Program g_sgangle_mpi, VERSION 4.5.3
Source code file: gmx_sgangle.c, line: 127

Fatal error:
Something wrong with contents of index file.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Did I make a error, what is the correct approach. to obtain the angle 
between 2 vectors ?




Per the description in g_sgangle -h, groups can only be two or three atoms in 
size.  It seems as if this tool would be very inefficient for any more than a 
few calculations.


-Justin


Thank you in advance

SA



--

Message: 3
Date: Wed, 16 Mar 2011 10:06:44 +0100
From: ?ngel Pi?eiro mailto:angel.pine...@usc.es>>
Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <1300266404.6843.29.camel@arginine>
Content-Type: text/plain; charset="utf-8"

Then, please, let us know how it works for your systems. The results for
my systems were exactly as expected. This allows to evaluate the order
of the C-chains regardless their orientation... but I do not know if
there is a better method to do this. I would be happy to know the
opinion of anyone else who want to try this or to propose an alternative
method.

Cheers,

à ngel.



On Wed, 2011-03-16 at 09:42 +0100, sa wrote:

 > Thank you Angel, I will try your suggestion.
 >
 > Cheers
 >
 > SA
 >
 >
 >
 >
 > Hi
 > very recently I faced the same problem with a system that
 > gives micelles
 > of different geometries and, as far as I saw, g_order
don't do
 > that.
 > Then I decided to compute a kind of local order parameters
 > defined as:
 >
 > S_i=(3 cos(\theta)-1)/2
 >
 > where theta is the angle between the segments joining the
 > carbon atoms
 > (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find
 > this
 > reasonable for your analysis...
 >
 > Cheers,
 >
 > Ã ngel.
 >
 >




--


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] Pressure Fluctuations

[Kavyashree M]

Thank you Sir

   I am using OPLSAA with tip4p water model, I agree to the fact that
it will oscillate but the oscillation is this case was from appr. -1000bar
to 1000bar. And as it is stated in the FAQ regarding the variation of
fluctuations with number of waters, this system has 6882 waters along
with a protein of 123 aa, so is not this fluctuations high?
   Pressure coupling used -parinello-rahman
  tau_p = 2.0
  tau_t  = 1.0
  compressibility 4.5e-5
  Pcouple_type = isotropic

Any suggestions?

Thanking you
With Regards
M. Kavyashree

On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham wrote:

>
>
> On 16/03/11, *Kavyashree M *  wrote:
>
> Dear users,
>
> Upon was trying to simulate an npt ensemble (protein in water),
> pressure was coupled using  parinello rahman system with tau_p = 2,
> tau_t = 1; compressibility 4.5e-5, type = isotropic.
>
> (cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9;
> rcoulomb = 1.2; rlist = 1.2).
>
> No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5), the
> pressure
> fluctuations are very drastic. I have gone through the mailing list
> regarding
> this issue but could not come to any conclusion.
>
> Any suggestions are helpfull.
>
> This is one of the statistics for pressure fluctuations.
>
> Statistics over 51 steps [ 0. through 1000. ps ], 1 data sets
> All statistics are over 11 points
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Pressure5.77629   0.99398.013   -5.34218  (bar)
>
>
> Looks very normal. See http://www.gromacs.org/Documentation/FAQs number 3
>
> Mark
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Re: [gmx-users] Pressure Fluctuations

[Justin A. Lemkul]

Kavyashree M wrote:

Thank you Sir

   I am using OPLSAA with tip4p water model, I agree to the fact that
it will oscillate but the oscillation is this case was from appr. -1000bar
to 1000bar. And as it is stated in the FAQ regarding the variation of
fluctuations with number of waters, this system has 6882 waters along
with a protein of 123 aa, so is not this fluctuations high?


No.  It is entirely expected, as you've been told.  Also pay attention to this 
statement from the page linked before:


"How much it varies and the speed at which it does depends on the type of 
pressure coupling used and the value of the coupling constants."


You may not see the exact same behavior described on the Pressure page if you're 
using different settings.


There is no problem here.

-Justin


   Pressure coupling used -parinello-rahman
  tau_p = 2.0
  tau_t  = 1.0
  compressibility 4.5e-5
  Pcouple_type = isotropic

Any suggestions?

Thanking you
With Regards
M. Kavyashree

On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham > wrote:




On 16/03/11, *Kavyashree M * mailto:hmkv...@gmail.com>> wrote:

Dear users,

Upon was trying to simulate an npt ensemble (protein in water),
pressure was coupled using  parinello rahman system with tau_p = 2,
tau_t = 1; compressibility 4.5e-5, type = isotropic.

(cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9;
rcoulomb = 1.2; rlist = 1.2).

No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5),
the pressure
fluctuations are very drastic. I have gone through the mailing
list regarding
this issue but could not come to any conclusion.

Any suggestions are helpfull.

This is one of the statistics for pressure fluctuations.

Statistics over 51 steps [ 0. through 1000. ps ], 1
data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Pressure5.77629   0.99398.013  
-5.34218  (bar)


Looks very normal. See http://www.gromacs.org/Documentation/FAQs
number 3

Mark
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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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Re: [gmx-users] Re: g_hbond output

[Erik Marklund]

ZHAO Lina skrev 2011-03-16 06.33:

@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 0   0   0
   200   0   0
   400   2   1
   600   0   3
   800   0   2
  1000   1   0
:
 5   3   2

Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 
if the $3 means pairs.


I tried pymol, and on the last frame,
there were 4 hydrogen bonds, between 7 residues. it's different from 
here 3 2
Last time I checked there's no hbond tool in pymol (although that may 
have changed without me knowing it). I have seen scrpts that does it for 
you, but they didn't take angles into account. Hence, different criteria 
may explain the discrepancy.


Thanks and sorry for last email without my realization it sent.

lina



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---
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
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Re: [gmx-users] Re: g_hbond output

[Erik Marklund]

Erik Marklund skrev 2011-03-16 16.25:

ZHAO Lina skrev 2011-03-16 06.33:

@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 0   0   0
   200   0   0
   400   2   1
   600   0   3
   800   0   2
  1000   1   0
:
 5   3   2

Here the situations, what's the $2 and $3 mean, why when $1=1000, 
$3=0 if the $3 means pairs.


I tried pymol, and on the last frame,
there were 4 hydrogen bonds, between 7 residues. it's different from 
here 3 2
Last time I checked there's no hbond tool in pymol (although that may 
have changed without me knowing it). I have seen scrpts that does it 
for you, but they didn't take angles into account. Hence, different 
criteria may explain the discrepancy.
I should add that there are issues with the current version of g_hbond, 
and I'm trying to find the time to fix them, but I'm in the process of 
finalizing my thesis, so I won't do it right away.


Thanks and sorry for last email without my realization it sent.

lina






--
---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] g_order for DPC alkyl chain in the micelle

[Ángel Piñeiro]

Dear SA
To be honest I am not sure this can be done by using g_angle, I used my
own code for this calculation. I could send it to you if you send me a
message off the list... but I would prefer to talk with a non-anonymous.

Cheers,

Ángel.




On Wed, 2011-03-16 at 15:58 +0100, sa wrote:

> Hi all 
> 
> This message is related with my previous message (see below) about the
> calculation of the order value for the DPC alkyl chain in a micelle.
> So if I understand well the previous angel's message, I need to
> compute the theta angle between the 2 vectors defined by the (i-1,i+1)
> and (i, i+2). So for carbon atom C14, I have created an index file
> with two groups defined as following
> 
> aC14 | aC16  and aC14 | aC16 with make_ndx_mpi
> 
> and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 10 -e
> 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups.
> Unfortunately i obtain the following error 
> 
> Group C13_C15 contains the following atoms:
> Atomname 0: C13
> Atomname 1: C15
> Atomname 2: C13
> Atomname 3: C15
> Atomname 4: C13
> Atomname 5: C15
> Atomname 6: C13
> Atomname 7: C15
> Atomname 8: C13
> Atomname 9: C1
> ...
> 
> Group C14_C16 contains the following atoms:
> Atomname 0: C14
> Atomname 1: C16
> Atomname 2: C14
> Atomname 3: C16
> Atomname 4: C14
> 
> ...
> Atomname 105: C16
> Atomname 106: C14
> Atomname 107: C16
> 
> Careful: distance only makes sense in some situations.
> 
> Reading frame   0 time 10.000
> Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#
> 
> ---
> Program g_sgangle_mpi, VERSION 4.5.3
> Source code file: gmx_sgangle.c, line: 127
> 
> Fatal error:
> Something wrong with contents of index file.
> 
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Did I make a error, what is the correct approach. to obtain the angle
> between 2 vectors ?
> 
> Thank you in advance 
> 
> SA
> 
> 
> 
> 
> --
> 
> Message: 3
> Date: Wed, 16 Mar 2011 10:06:44 +0100
> From: ?ngel Pi?eiro 
> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue
> 106
> To: Discussion list for GROMACS users 
> Message-ID: <1300266404.6843.29.camel@arginine>
> Content-Type: text/plain; charset="utf-8"
> 
> Then, please, let us know how it works for your systems. The
> results for
> my systems were exactly as expected. This allows to evaluate
> the order
> of the C-chains regardless their orientation... but I do not
> know if
> there is a better method to do this. I would be happy to know
> the
> opinion of anyone else who want to try this or to propose an
> alternative
> method.
> 
> Cheers,
> 
> Ã ngel.
> 
> 
> 
> On Wed, 2011-03-16 at 09:42 +0100, sa wrote:
> 
> > Thank you Angel, I will try your suggestion.
> >
> > Cheers
> >
> > SA
> >
> >
> >
> >
> > Hi
> > very recently I faced the same problem with a system
> that
> > gives micelles
> > of different geometries and, as far as I saw,
> g_order don't do
> > that.
> > Then I decided to compute a kind of local order
> parameters
> > defined as:
> >
> > S_i=(3 cos(\theta)-1)/2
> >
> > where theta is the angle between the segments
> joining the
> > carbon atoms
> > (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps
> you find
> > this
> > reasonable for your analysis...
> >
> > Cheers,
> >
> > Ã ngel.
> >
> >
> 
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at 
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[gmx-users] Re: g_order for DPC alkyl chain in the micelle

[sa]

Ok Justin,

So which gmx tool i can use to obtain the angle between two vectors defined
by two atom pairs ?

SA


sa wrote:
> > Hi all
> >
> > This message is related with my previous message (see below) about the
> > calculation of the order value for the DPC alkyl chain in a micelle. So
> > if I understand well the previous angel's message, I need to compute the
> > theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2).
> > So for carbon atom C14, I have created an index file with two groups
> > defined as following
> >
> > aC14 | aC16  and aC14 | aC16 with make_ndx_mpi
> >
> > and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 10 -e
> > 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups.
> > Unfortunately i obtain the following error
> >
> > Group C13_C15 contains the following atoms:
> > Atomname 0: C13
> > Atomname 1: C15
> > Atomname 2: C13
> > Atomname 3: C15
> > Atomname 4: C13
> > Atomname 5: C15
> > Atomname 6: C13
> > Atomname 7: C15
> > Atomname 8: C13
> > Atomname 9: C1
> > ...
> >
> > Group C14_C16 contains the following atoms:
> > Atomname 0: C14
> > Atomname 1: C16
> > Atomname 2: C14
> > Atomname 3: C16
> > Atomname 4: C14
> >
> > ...
> > Atomname 105: C16
> > Atomname 106: C14
> > Atomname 107: C16
> >
> > Careful: distance only makes sense in some situations.
> >
> > Reading frame   0 time 10.000
> > Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#
> >
> > ---
> > Program g_sgangle_mpi, VERSION 4.5.3
> > Source code file: gmx_sgangle.c, line: 127
> >
> > Fatal error:
> > Something wrong with contents of index file.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> >
> > Did I make a error, what is the correct approach. to obtain the angle
> > between 2 vectors ?
> >
>
> Per the description in g_sgangle -h, groups can only be two or three atoms
> in
> size.  It seems as if this tool would be very inefficient for any more than
> a
> few calculations.
>
> -Justin
>
> > Thank you in advance
> >
> > SA
> >
> >
> >
> > --
> >
> > Message: 3
> > Date: Wed, 16 Mar 2011 10:06:44 +0100
> > From: ?ngel Pi?eiro  angel.pine...@usc.es>>
> > Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
> > To: Discussion list for GROMACS users  > >
> > Message-ID: <1300266404.6843.29.camel@arginine>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Then, please, let us know how it works for your systems. The results
> for
> > my systems were exactly as expected. This allows to evaluate the
> order
> > of the C-chains regardless their orientation... but I do not know if
> > there is a better method to do this. I would be happy to know the
> > opinion of anyone else who want to try this or to propose an
> alternative
> > method.
> >
> > Cheers,
> >
> > Ã ngel.
> >
> >
> >
> > On Wed, 2011-03-16 at 09:42 +0100, sa wrote:
> >
> >  > Thank you Angel, I will try your suggestion.
> >  >
> >  > Cheers
> >  >
> >  > SA
> >  >
> >  >
> >  >
> >  >
> >  > Hi
> >  > very recently I faced the same problem with a system that
> >  > gives micelles
> >  > of different geometries and, as far as I saw, g_order
> > don't do
> >  > that.
> >  > Then I decided to compute a kind of local order parameters
> >  > defined as:
> >  >
> >  > S_i=(3 cos(\theta)-1)/2
> >  >
> >  > where theta is the angle between the segments joining the
> >  > carbon atoms
> >  > (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you
> find
> >  > this
> >  > reasonable for your analysis...
> >  >
> >  > Cheers,
> >  >
> >  > Ã ngel.
> >  >
> >  >
> >
> >
>
> --
> 
>
> 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] Density of methanol too low

[Jesús Carrete Montaña]

Dear list members,

   I am running some simple simulations of pure ethanol and methanol using
the opls-aa force field as implemented in GROMACS 4.5.3, as a test case
before attempting to study mixtures with more complex molecules. My
problem is that, even though there are published results [1] that show
that this force field can yield satisfatory estimates of the density of
methanol, I am getting an average density around 745 kg/m3, much lower
than the expected 786 kg/m3.
   Attached you can find all the relevant imput files (em.mdp is for the
initial energy minimization, stab.mdp for the "stabilization" run and
run.mdp for the "production" run; sample methanol.gro only contains one
molecule). I got good results for ethanol and ethanol/water mixtures using
basically the same set of mdp files, so I suspect the problem is in my
input .gro file, but I haven't been able to spot it. I would be thankful
for any help you could provide.

Best wishes,
Jesús

[1] G. Kaminski and W. L. Jorgensen, J. Phys. Chem. 1996, 100, 18010-18013.


topol.top
Description: Binary data


stab.mdp
Description: Binary data


run.mdp
Description: Binary data


em.mdp
Description: Binary data


methanol.gro
Description: Binary data
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Re: [gmx-users] Density of methanol too low

[David van der Spoel]

On 2011-03-16 16.35, Jesús Carrete Montaña wrote:

Dear list members,

I am running some simple simulations of pure ethanol and methanol using
the opls-aa force field as implemented in GROMACS 4.5.3, as a test case
before attempting to study mixtures with more complex molecules. My
problem is that, even though there are published results [1] that show
that this force field can yield satisfatory estimates of the density of
methanol, I am getting an average density around 745 kg/m3, much lower
than the expected 786 kg/m3.
Attached you can find all the relevant imput files (em.mdp is for the
initial energy minimization, stab.mdp for the "stabilization" run and
run.mdp for the "production" run; sample methanol.gro only contains one
molecule). I got good results for ethanol and ethanol/water mixtures using
basically the same set of mdp files, so I suspect the problem is in my
input .gro file, but I haven't been able to spot it. I would be thankful
for any help you could provide.

Best wishes,
Jesús

[1] G. Kaminski and W. L. Jorgensen, J. Phys. Chem. 1996, 100, 18010-18013.

Check Wensink et al. JCP 119 (2003) 7308. Did you turn on PME, 
dispersion correction etc?


--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] Pressure Fluctuations

[Kavyashree M]

Thank you Justin,

   When I went through most of the mailing list the fluctuations are not so
high
and even in the FAQ it was mentioned in the range of 500-600 bar for 216
water.
And more over the average pressure was ~6bar instead of 1bar which was
required.

  So would you suggest that I can proceed with this file for the production
run without
any problem. I was following your lysozyme tutorial where fluctuations were
much
less.. hence I suspected some problem in this data.

Thanking you
With regards
M. Kavyashree


On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Thank you Sir
>>
>>   I am using OPLSAA with tip4p water model, I agree to the fact that
>> it will oscillate but the oscillation is this case was from appr. -1000bar
>> to 1000bar. And as it is stated in the FAQ regarding the variation of
>> fluctuations with number of waters, this system has 6882 waters along
>> with a protein of 123 aa, so is not this fluctuations high?
>>
>
> No.  It is entirely expected, as you've been told.  Also pay attention to
> this statement from the page linked before:
>
> "How much it varies and the speed at which it does depends on the type of
> pressure coupling used and the value of the coupling constants."
>
> You may not see the exact same behavior described on the Pressure page if
> you're using different settings.
>
> There is no problem here.
>
> -Justin
>
>Pressure coupling used -parinello-rahman
>>  tau_p = 2.0
>>  tau_t  = 1.0
>>  compressibility 4.5e-5
>>  Pcouple_type = isotropic
>>
>> Any suggestions?
>>
>> Thanking you
>> With Regards
>> M. Kavyashree
>>
>> On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham 
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>
>>
>>On 16/03/11, *Kavyashree M * >> wrote:
>>
>>>Dear users,
>>>
>>>Upon was trying to simulate an npt ensemble (protein in water),
>>>pressure was coupled using  parinello rahman system with tau_p = 2,
>>>tau_t = 1; compressibility 4.5e-5, type = isotropic.
>>>
>>>(cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9;
>>>rcoulomb = 1.2; rlist = 1.2).
>>>
>>>No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5),
>>>the pressure
>>>fluctuations are very drastic. I have gone through the mailing
>>>list regarding
>>>this issue but could not come to any conclusion.
>>>
>>>Any suggestions are helpfull.
>>>
>>>This is one of the statistics for pressure fluctuations.
>>>
>>>Statistics over 51 steps [ 0. through 1000. ps ], 1
>>>data sets
>>>All statistics are over 11 points
>>>
>>>Energy  Average   Err.Est.   RMSD  Tot-Drift
>>>
>>>  
>>> ---
>>>Pressure5.77629   0.99398.013
>>>  -5.34218  (bar)
>>>
>>
>>Looks very normal. See http://www.gromacs.org/Documentation/FAQs
>>number 3
>>
>>Mark
>>--
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>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>.
>>
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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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[gmx-users] dipole moment autocorrelation function

[Nilesh Dhumal]

Hello,

I am trying to calculate the non normalized dipole moment autocorrelation
function for water. I am using flexible spc water model
(define=-DFLEX_SPC). I am using gromacs 4.0.7 version.

I run the simulation for 200 ps.  I run the following command to calculate
 the dipole moment autocorrelation function

 g_dipoles -f water.trr -s water.tpr -nonormalize -corr total -c

I am geting the value really high (dipcorr.xvg). I pasted some of them. Is
there anything wrong or the values are high becuase its not normalized.

Thanks

Nilesh

 0.000  4619.40918
 0.001  4619.04248
 0.002  4617.97412
 0.003  4616.21973
 0.004  4613.80176

99.997  -121.73769
99.998  -121.75319
99.999  -121.77924
100.000  -121.81487


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Re: [gmx-users] Re: g_order for DPC alkyl chain in the micelle

[Justin A. Lemkul]

sa wrote:

Ok Justin,

So which gmx tool i can use to obtain the angle between two vectors 
defined by two atom pairs ?




Well, that's what g_sgangle does.  What I said was that if you have to do this 
more than a few times (since you have to do every pair of atoms separately), 
this can be quite tedious, especially if you have multiple molecules with 
multiple angles to calculate.


-Justin


SA


sa wrote:
 > Hi all
 >
 > This message is related with my previous message (see below)
about the
 > calculation of the order value for the DPC alkyl chain in a
micelle. So
 > if I understand well the previous angel's message, I need to
compute the
 > theta angle between the 2 vectors defined by the (i-1,i+1) and
(i, i+2).
 > So for carbon atom C14, I have created an index file with two groups
 > defined as following
 >
 > aC14 | aC16  and aC14 | aC16 with make_ndx_mpi
 >
 > and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 10 -e
 > 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups.
 > Unfortunately i obtain the following error
 >
 > Group C13_C15 contains the following atoms:
 > Atomname 0: C13
 > Atomname 1: C15
 > Atomname 2: C13
 > Atomname 3: C15
 > Atomname 4: C13
 > Atomname 5: C15
 > Atomname 6: C13
 > Atomname 7: C15
 > Atomname 8: C13
 > Atomname 9: C1
 > ...
 >
 > Group C14_C16 contains the following atoms:
 > Atomname 0: C14
 > Atomname 1: C16
 > Atomname 2: C14
 > Atomname 3: C16
 > Atomname 4: C14
 >
 > ...
 > Atomname 105: C16
 > Atomname 106: C14
 > Atomname 107: C16
 >
 > Careful: distance only makes sense in some situations.
 >
 > Reading frame   0 time 10.000
 > Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#
 >
 > ---
 > Program g_sgangle_mpi, VERSION 4.5.3
 > Source code file: gmx_sgangle.c, line: 127
 >
 > Fatal error:
 > Something wrong with contents of index file.
 >
 > For more information and tips for troubleshooting, please check
the GROMACS
 > website at http://www.gromacs.org/Documentation/Errors
 > ---
 >
 > Did I make a error, what is the correct approach. to obtain the angle
 > between 2 vectors ?
 >

Per the description in g_sgangle -h, groups can only be two or three
atoms in
size.  It seems as if this tool would be very inefficient for any
more than a
few calculations.

-Justin

 > Thank you in advance
 >
 > SA
 >
 >
 >
 > --
 >
 > Message: 3
 > Date: Wed, 16 Mar 2011 10:06:44 +0100
 > From: ?ngel Pi?eiro mailto:angel.pine...@usc.es> >>
 > Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
 > To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>
 > >>
 > Message-ID: <1300266404.6843.29.camel@arginine>
 > Content-Type: text/plain; charset="utf-8"
 >
 > Then, please, let us know how it works for your systems. The
results for
 > my systems were exactly as expected. This allows to evaluate
the order
 > of the C-chains regardless their orientation... but I do not
know if
 > there is a better method to do this. I would be happy to know the
 > opinion of anyone else who want to try this or to propose an
alternative
 > method.
 >
 > Cheers,
 >
 > Ã ngel.
 >
 >
 >
 > On Wed, 2011-03-16 at 09:42 +0100, sa wrote:
 >
 >  > Thank you Angel, I will try your suggestion.
 >  >
 >  > Cheers
 >  >
 >  > SA
 >  >
 >  >
 >  >
 >  >
 >  > Hi
 >  > very recently I faced the same problem with a
system that
 >  > gives micelles
 >  > of different geometries and, as far as I saw, g_order
 > don't do
 >  > that.
 >  > Then I decided to compute a kind of local order
parameters
 >  > defined as:
 >  >
 >  > S_i=(3 cos(\theta)-1)/2
 >  >
 >  > where theta is the angle between the segments
joining the
 >  > carbon atoms
 >  > (i-1,i+1) and (i, i+2) in a linear C-chain.
Perhaps you find
 >  > this
 >  > reasonable for your analysis...
 >  >
 >  > Cheers,
 >  >
 >  > Ã ngel.
 >  >
 >  >
 >
 >

--
==

Re: [gmx-users] Pressure Fluctuations

[Justin A. Lemkul]

Kavyashree M wrote:

Thank you Justin,

   When I went through most of the mailing list the fluctuations are not 
so high
and even in the FAQ it was mentioned in the range of 500-600 bar for 216 
water.


You cannot always assume that rules of thumb and others' results will (or 
should) necessarily match your own.  Unless you are using identical input files, 
you won't necessarily get the same results.  Much of the fluctuation information 
is probably based on the Berendsen thermostat, which does not oscillate as much 
as Parrinello-Rahman.  Other factors in the .mdp file will influence these 
statistics, since both the kinetic energy of the system and the virial are used 
to calculate pressure (see the manual).


And more over the average pressure was ~6bar instead of 1bar which was 
required.




And with fluctuations +/- 1000, is 6 really all that different from 1?  There 
was an extensive discussion some time back about this.  I would suggest you have 
a look through the archive.


  So would you suggest that I can proceed with this file for the 
production run without
any problem. I was following your lysozyme tutorial where fluctuations 
were much

less.. hence I suspected some problem in this data.



The lysozyme system has nearly twice the number of waters that your system has 
(over 10,000), hence the fluctuations will be much smaller, and even then, the 
pressure oscillates by +/- 400 or so.


Again, I see no problem here.  What you report is what is to be expected.

-Justin


Thanking you
With regards
M. Kavyashree


On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Thank you Sir

  I am using OPLSAA with tip4p water model, I agree to the fact that
it will oscillate but the oscillation is this case was from
appr. -1000bar
to 1000bar. And as it is stated in the FAQ regarding the
variation of
fluctuations with number of waters, this system has 6882 waters
along
with a protein of 123 aa, so is not this fluctuations high?


No.  It is entirely expected, as you've been told.  Also pay
attention to this statement from the page linked before:

"How much it varies and the speed at which it does depends on the
type of pressure coupling used and the value of the coupling constants."

You may not see the exact same behavior described on the Pressure
page if you're using different settings.

There is no problem here.

-Justin

  Pressure coupling used -parinello-rahman
 tau_p = 2.0
 tau_t  = 1.0
 compressibility 4.5e-5
 Pcouple_type = isotropic

Any suggestions?

Thanking you
With Regards
M. Kavyashree

On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:



   On 16/03/11, *Kavyashree M * mailto:hmkv...@gmail.com>
   >> wrote:

   Dear users,

   Upon was trying to simulate an npt ensemble (protein in
water),
   pressure was coupled using  parinello rahman system with
tau_p = 2,
   tau_t = 1; compressibility 4.5e-5, type = isotropic.

   (cut off scheme (vdw_type = switch; rvdw = 1.0;
rvdw_switch = 0.9;
   rcoulomb = 1.2; rlist = 1.2).

   No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3,
3.5),
   the pressure
   fluctuations are very drastic. I have gone through the
mailing
   list regarding
   this issue but could not come to any conclusion.

   Any suggestions are helpfull.

   This is one of the statistics for pressure fluctuations.

   Statistics over 51 steps [ 0. through 1000.
ps ], 1
   data sets
   All statistics are over 11 points

   Energy  Average   Err.Est.   RMSD
 Tot-Drift
 
 ---

   Pressure5.77629   0.99398.013
 -5.34218  (bar)


   Looks very normal. See http://www.gromacs.org/Documentation/FAQs
   number 3

   Mark
   --
   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.

[gmx-users] Pulling

[chris . neale]

2-When you limit your sampling phase space,it can make some Errors,
Because you may ignore some important regions(where you don't know  
them and you can't predict there).


I agree with the idea that underlies your point, but it is not a  
problem. You don't need to sample all intervening phase space, just  
converge one well defined part of it. Read that paper again, and some  
others.


... snip ...


Is it possible to do Umbrella Sampling while the drug be free to rotate
along with oscilation in windows?


sure, but you will have more convergence problems.

Chris.

On Tue, Mar 15, 2011 at 9:49 AM,  wrote:


1. yes. it is acceptable. It is different, but neither method is de facto
better.

2. to enhance convergence by limiting the amount of phase space that must
be sampled. Changing the restraints can change the profile, but if you care
only about the integrated standard binding free energy then it does not
change the converged result. See, for example, D. L. Mobley, J. D. Chodera,
K. A. Dill. "On the use of orientational restraints and symmetry number
corrections in alchemical free energy calculations", ...

Chris.

-- original message --

Dear All
Afew question about Pulling in Umberella Sampling

1-the goal of pulling is making some primary structures (in different
distances) to do umberella sampling for each one of them.
 I can make these states by transporting my ligands along a vector to
prepare these primary structures.Is this correct?Now I can do US for each
one!without any need to doing pulling.

2-Why do we keep fix the relative orientation of Protein-ligand during the
pulling ? I think changing the orientation of ligand during the
pulling(suppose the protein is restrain) can chang our result?
 Because our umbrella sampling maintain this orientation too.am I right?

Thanks in advance
-- next part --



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Re: [gmx-users] Pressure Fluctuations

[Kavyashree M]

Thank you Justin!

On Wed, Mar 16, 2011 at 9:28 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Thank you Justin,
>>
>>   When I went through most of the mailing list the fluctuations are not so
>> high
>> and even in the FAQ it was mentioned in the range of 500-600 bar for 216
>> water.
>>
>
> You cannot always assume that rules of thumb and others' results will (or
> should) necessarily match your own.  Unless you are using identical input
> files, you won't necessarily get the same results.  Much of the fluctuation
> information is probably based on the Berendsen thermostat, which does not
> oscillate as much as Parrinello-Rahman.  Other factors in the .mdp file will
> influence these statistics, since both the kinetic energy of the system and
> the virial are used to calculate pressure (see the manual).
>
>
>  And more over the average pressure was ~6bar instead of 1bar which was
>> required.
>>
>>
> And with fluctuations +/- 1000, is 6 really all that different from 1?
>  There was an extensive discussion some time back about this.  I would
> suggest you have a look through the archive.
>
>
>   So would you suggest that I can proceed with this file for the production
>> run without
>> any problem. I was following your lysozyme tutorial where fluctuations
>> were much
>> less.. hence I suspected some problem in this data.
>>
>>
> The lysozyme system has nearly twice the number of waters that your system
> has (over 10,000), hence the fluctuations will be much smaller, and even
> then, the pressure oscillates by +/- 400 or so.
>
> Again, I see no problem here.  What you report is what is to be expected.
>
> -Justin
>
>  Thanking you
>> With regards
>> M. Kavyashree
>>
>>
>> On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Kavyashree M wrote:
>>
>>Thank you Sir
>>
>>  I am using OPLSAA with tip4p water model, I agree to the fact
>> that
>>it will oscillate but the oscillation is this case was from
>>appr. -1000bar
>>to 1000bar. And as it is stated in the FAQ regarding the
>>variation of
>>fluctuations with number of waters, this system has 6882 waters
>>along
>>with a protein of 123 aa, so is not this fluctuations high?
>>
>>
>>No.  It is entirely expected, as you've been told.  Also pay
>>attention to this statement from the page linked before:
>>
>>"How much it varies and the speed at which it does depends on the
>>type of pressure coupling used and the value of the coupling
>> constants."
>>
>>You may not see the exact same behavior described on the Pressure
>>page if you're using different settings.
>>
>>There is no problem here.
>>
>>-Justin
>>
>>  Pressure coupling used -parinello-rahman
>> tau_p = 2.0
>> tau_t  = 1.0
>> compressibility 4.5e-5
>> Pcouple_type = isotropic
>>
>>Any suggestions?
>>
>>Thanking you
>>With Regards
>>M. Kavyashree
>>
>>On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>>>>> wrote:
>>
>>
>>
>>   On 16/03/11, *Kavyashree M * >
>>   >> wrote:
>>
>>   Dear users,
>>
>>   Upon was trying to simulate an npt ensemble (protein in
>>water),
>>   pressure was coupled using  parinello rahman system with
>>tau_p = 2,
>>   tau_t = 1; compressibility 4.5e-5, type = isotropic.
>>
>>   (cut off scheme (vdw_type = switch; rvdw = 1.0;
>>rvdw_switch = 0.9;
>>   rcoulomb = 1.2; rlist = 1.2).
>>
>>   No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3,
>>3.5),
>>   the pressure
>>   fluctuations are very drastic. I have gone through the
>>mailing
>>   list regarding
>>   this issue but could not come to any conclusion.
>>
>>   Any suggestions are helpfull.
>>
>>   This is one of the statistics for pressure fluctuations.
>>
>>   Statistics over 51 steps [ 0. through 1000.
>>ps ], 1
>>   data sets
>>   All statistics are over 11 points
>>
>>   Energy  Average   Err.Est.   RMSD
>> Tot-Drift
>>
>>  
>> ---
>>   Pressure5.77629   0.99398.013
>> -5.34218  (bar)
>>
>>
>>   Looks very normal. See
>> http://www.gromacs.org/Documentation/FAQs
>>   number 3
>>
>>   Mark
>>   --
>>   gmx-users mailing listgmx-users@gromacs.org
>>

[gmx-users] Umberella sampling

[chris . neale]

Mohsen:

To be honest, this just sounds like debating. I have offered you my  
perspective already.


Chris.

-- original message --

Dear chris
Thanks for your reply

1-I am not sure,Since we need the know the variations of free energy along a
specific degree of freedom of system(for example z axis),so  the springs
must be 1 dimensional to allow drug to oscilate only in one dimension(z
axis).
Let me say my question in other words:
Do we need to do sampling just in phase space related to z axis(1
dimensional) or we can do sampling in other places(if it be 3
dimensional),Although we still want the variation of free energy along z
axis?

2-evry windows have a width(for example 0.02 nm),Besides according to Hock's
law knowing the oscilation amplitude is possible when you have the K and the
mass and total energy:1/2 k(x/2)^2=1/2 m v(max)^2

3-my question in other words:
Since we need overlapping the distribution densities of each windows,Does
the drug need to enter to the neighbour windows a little ?
Thanks in advance for your reply
On Tue, Mar 15, 2011 at 9:54 AM,  wrote:


1. Depends on how you set them in your .mdp file. It could be either.

2. There is no general method. Use trial and error. Also, your question is
flawed, K defines X. Unless by "length of one windows" you meant the
distance between neighbouring centers of restraint (umbrellas).

3. you need overlapping distributions. Let's leave it at that. I have not
seen any general treatment of what K is required and I am rather sure that
it is impossible to predetermine the necessary force constants (K) unless
you know the PMF. If you need to know the PMF beforehand then this is not a
general solution and also probably useless since the whole purpose is to get
the PMF.

Chris.

-- original message --

Dear All



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[gmx-users] Website search down again

[Justin A. Lemkul]

Hi,

Just a heads-up, the Gromacs site search is not working again.  Instead of 
returning errors, it just comes up with "Your search did not return any 
results."  The mailing list search is working correctly.


-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] g_order for DPC alkyl chain in the micelle

[sa]

OK Angel,

I will contact you off-list

SA

>
> Dear SA
> To be honest I am not sure this can be done by using g_angle, I used my
> own code for this calculation. I could send it to you if you send me a
> message off the list... but I would prefer to talk with a non-anonymous.
>
> Cheers,
>
> Ã ngel.
>
>
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Re: [gmx-users] g_membed tool

[Igor Marques]

dear mohana,

please refer to this page ,
to this article
(g_membed:
Efficient Insertion of a Membrane Protein into an Equilibrated
Lipid Bilayer with Minimal Perturbation) or to this
manual,
that apparently compiles both the page and the article.

good luck,
  Igor Marques


On Wed, Mar 16, 2011 at 4:51 AM, Mohana lakshmi  wrote:

> Dear all..
>
> I am using g_membed tools to embed the protein into lipid membrane. I read
> that before doing g_membed we need to run a short run with some options in
> .mdp files.
> what are the steps do we need to do before g_membed. It is given that box
> size should be taken from the membrane strucuture file but i don t know how
> and where to mention the size?
> Whether any tutorial is available for transmembrane protein using g_membed
> tool?
>
> Thank you
>
> Mohanalakshmi N.
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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[gmx-users] g_rmsf

[simon sham]

Hi,
I am just curious that in the MD community whether there is consensus on how to 
compare calculated rmsfs and expermental b-factors in x-ray. Should we use 
average value per residue or one particular atom in a residue for comparsion. 
Secondly, in NMR, people minimize a number of final calculated structures with 
energy minimization. Do people do the same thing when they average their 
structures within a certain time period with g_rmsf or g-covar.

Thanks for your insight.

Simon Sham




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RE: [gmx-users] Memory allocation - xpm2ps

[Shi, Chuanyin]

Too bad, I am having this problem with 4.5 now.
The xpm file with larger size will counter this problem while smaller ones are 
fine.
Never had any problem with previous version.


Chuanyin Shi
Department of Chemistry & Biochemistry
University of Oklahoma


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, October 15, 2010 4:10 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Memory allocation - xpm2ps

Maurício Menegatti Rigo wrote:
> Hi,
>
> I copy the file gmx_xpm2ps from the repository to my gromacs folder
> /usl/local/gromacs/src/tools (i.e. I substitute the old file by the new
> one). After that, I run xpm2ps and the problem persisted.
>
> Any ideas?
>

As I said before, you have to actually re-compile and install the git version of
Gromacs to see any effect.  Further, simply replacing a file likely will not
work due to a multitude of code changes that have taken place in other source 
files.

> PS: I run the same job in another i7, but with gromacs version 4.0.7
> installed, and everything occured well.
>

Yes, there was a bug introduced in version 4.5.  Please either install the git
version properly, use xpm2ps included in version 4.0.7, or wait for the release
of version 4.5.2.

-Justin

>
> 2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu>>
>
>
>
> Maurício Menegatti Rigo wrote:
>
>
> Hi,
>
> Thank you for your answer. Unfortunately, I can't fix my problem.
> I dont know if I'm doing this right, but first I type the line
> "/git clone git://git.gromacs.org/gromacs.git
> 
> /" in the command line.
> After all the outputs, I tried to run xpm2ps again, but occured
> the same error.
>
>
> Simply downloading the source code won't fix the problem.  You have
> to install (and then use) the resulting binaries.
>
> -Justin
>
>
>
> 2010/10/15 Justin A. Lemkul    >>
>
>
>
>
>Maurício Menegatti Rigo wrote:
>
>Hi,
>I found the following error when I tried to run xpm2ps.
>
>
>*** glibc detected *** xpm2ps: realloc(): invalid pointer:
>0x00dd0541 ***
>=== Backtrace: =
>/lib/libc.so.6[0x7f20a53b0dd6]
>/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
>xpm2ps(save_realloc+0x5e)[0x43741e]
>xpm2ps[0x42cf24]
>xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
>xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
>xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
>/lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
>xpm2ps[0x412949]
>=== Memory map: 
>0040-005e3000 r-xp  fc:03 7799252
>   /usr/local/gromacs/bin/xpm2ps
>007e2000-007e3000 r-xp 001e2000 fc:03 7799252
>   /usr/local/gromacs/bin/xpm2ps
>007e3000-007e9000 rwxp 001e3000 fc:03 7799252
>   /usr/local/gromacs/bin/xpm2ps
>007e9000-007ea000 rwxp  00:00 0 00dce000-00def000
> rwxp
> 00:00 0  [heap]
>7f20a5124000-7f20a513a000 r-xp  fc:03 17400029
>/lib/libgcc_s.so.1
>7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029
>/lib/libgcc_s.so.1
>7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029
>/lib/libgcc_s.so.1
>7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029
>/lib/libgcc_s.so.1
>7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032
>/lib/libc-2.10.1.so
>  
>
>7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032
>/lib/libc-2.10.1.so
>  
>
>7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032
>/lib/libc-2.10.1.so
>  
>
>7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032
>/lib/libc-2.10.1.so
>  
>
>7f20a56a5000-7f20a56aa000 rwxp 000

Re: [gmx-users] Memory allocation - xpm2ps

[Justin A. Lemkul]

Shi, Chuanyin wrote:

Too bad, I am having this problem with 4.5 now.


Version 4.5 contains the bug referenced below and was only fixed as of 4.5.2, so 
make sure you're using the newest version (4.5.3) when reporting problems.  In 
general, fixing problems in old versions is not a high priority, especially if 
they may already be fixed in an official release.



The xpm file with larger size will counter this problem while smaller ones are 
fine.
Never had any problem with previous version.



Depending on the amount of memory available on your machine, this could be a 
Gromacs problem, a hardware problem, or a combination of both.  Please test the 
latest version of Gromacs (4.5.3) and report back with some diagnostic 
information (i.e., size of the files that do and don't work, hardware, available 
memory, etc).


-Justin



Chuanyin Shi
Department of Chemistry & Biochemistry
University of Oklahoma


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, October 15, 2010 4:10 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Memory allocation - xpm2ps

Maurício Menegatti Rigo wrote:

Hi,

I copy the file gmx_xpm2ps from the repository to my gromacs folder
/usl/local/gromacs/src/tools (i.e. I substitute the old file by the new
one). After that, I run xpm2ps and the problem persisted.

Any ideas?



As I said before, you have to actually re-compile and install the git version of
Gromacs to see any effect.  Further, simply replacing a file likely will not
work due to a multitude of code changes that have taken place in other source 
files.


PS: I run the same job in another i7, but with gromacs version 4.0.7
installed, and everything occured well.



Yes, there was a bug introduced in version 4.5.  Please either install the git
version properly, use xpm2ps included in version 4.0.7, or wait for the release
of version 4.5.2.

-Justin


2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu>>



Maurício Menegatti Rigo wrote:


Hi,

Thank you for your answer. Unfortunately, I can't fix my problem.
I dont know if I'm doing this right, but first I type the line
"/git clone git://git.gromacs.org/gromacs.git

/" in the command line.
After all the outputs, I tried to run xpm2ps again, but occured
the same error.


Simply downloading the source code won't fix the problem.  You have
to install (and then use) the resulting binaries.

-Justin



2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu> >>




   Maurício Menegatti Rigo wrote:

   Hi,
   I found the following error when I tried to run xpm2ps.


   *** glibc detected *** xpm2ps: realloc(): invalid pointer:
   0x00dd0541 ***
   === Backtrace: =
   /lib/libc.so.6[0x7f20a53b0dd6]
   /lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
   xpm2ps(save_realloc+0x5e)[0x43741e]
   xpm2ps[0x42cf24]
   xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
   xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
   xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
   /lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
   xpm2ps[0x412949]
   === Memory map: 
   0040-005e3000 r-xp  fc:03 7799252
  /usr/local/gromacs/bin/xpm2ps
   007e2000-007e3000 r-xp 001e2000 fc:03 7799252
  /usr/local/gromacs/bin/xpm2ps
   007e3000-007e9000 rwxp 001e3000 fc:03 7799252
  /usr/local/gromacs/bin/xpm2ps
   007e9000-007ea000 rwxp  00:00 0 00dce000-00def000
rwxp
    00:00 0  [heap]
   7f20a5124000-7f20a513a000 r-xp  fc:03 17400029
   /lib/libgcc_s.so.1
   7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029
   /lib/libgcc_s.so.1
   7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029
   /lib/libgcc_s.so.1
   7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029
   /lib/libgcc_s.so.1
   7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032
   /lib/libc-2.10.1.so
 
   
   7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032
   /lib/libc-2.10.1.so
 
   

[gmx-users] lipopeptide problem

[Emine Deniz Tekin]

Hi GROMACS Users,

I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I
simulated a peptide before but this is the first time I am trying to combine
a lipid with a peptide (to get a lipo-peptide). I would be really happy if
you could help me out with the following question

I am tring to create a louroic acid connected to and an 8-redidue peptide.
To create residues, I used ARGUSLAB . For the louric acid I used BERGER
lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined
ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the
topol.top files as described in the manual. But this procedure did not yet
give me an attached louric acid and peptide. I still have to play with the
aminoacids.hdb, aminoacids.rtp, residuetypes.dat, atomtypes.atp, and
specbond.dat files. I would appreciate if you could let me know how to
modify these files, especially the aminoacids.hdb file. I tried several
things but it not work. Note that, I applied the suggestions in
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
but it was not sufficient.

Best regards

Deniz
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Re: [gmx-users] lipopeptide problem

[Justin A. Lemkul]

Emine Deniz Tekin wrote:

Hi GROMACS Users,

I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I 
simulated a peptide before but this is the first time I am trying to 
combine a lipid with a peptide (to get a lipo-peptide). I would be 
really happy if you could help me out with the following question


I am tring to create a louroic acid connected to and an 8-redidue 
peptide. To create residues, I used ARGUSLAB . For the louric acid I 
used BERGER lipid parameters. Then, as described in KALP-15 in DPPC 
tutorial, I combined ffbonded.itp and ffnonbonded.itp with lipid.itp. I 
also adjusted the topol.top files as described in the manual. But this 
procedure did not yet give me an attached louric acid and peptide. I 


Nor should you expect it to.  Building the parent force field does not give you 
a topology describing some molecular system.


still have to play with the aminoacids.hdb, aminoacids.rtp, 
residuetypes.dat, atomtypes.atp, and specbond.dat files. I would 
appreciate if you could let me know how to modify these files, 
especially the aminoacids.hdb file. I tried several things but it not 


See the manual, section 5.6.4.  The contents and format are discussed at length.

work. Note that, I applied the suggestions 
in http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, 
but it was not sufficient.




If you want free help, you will have to do substantially better than "it was not 
sufficient."  What is not clear?  What have you tried and what was the result? 
If you want free help, you've got to demonstrate a willingness to do some work 
on your own.


-Justin


Best regards

Deniz



--


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] Memory allocation - xpm2ps

[Shi, Chuanyin]

Ye, I just installed the 4.5.3 and the problem is gone.
I was using the 4.5.1 before.


Chuanyin Shi
Department of Chemistry & Biochemistry
University of Oklahoma


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, March 16, 2011 4:20 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] Memory allocation - xpm2ps

Shi, Chuanyin wrote:
> Too bad, I am having this problem with 4.5 now.

Version 4.5 contains the bug referenced below and was only fixed as of 4.5.2, so
make sure you're using the newest version (4.5.3) when reporting problems.  In
general, fixing problems in old versions is not a high priority, especially if
they may already be fixed in an official release.

> The xpm file with larger size will counter this problem while smaller ones 
> are fine.
> Never had any problem with previous version.
>

Depending on the amount of memory available on your machine, this could be a
Gromacs problem, a hardware problem, or a combination of both.  Please test the
latest version of Gromacs (4.5.3) and report back with some diagnostic
information (i.e., size of the files that do and don't work, hardware, available
memory, etc).

-Justin

>
> Chuanyin Shi
> Department of Chemistry & Biochemistry
> University of Oklahoma
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Friday, October 15, 2010 4:10 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Memory allocation - xpm2ps
>
> Maurício Menegatti Rigo wrote:
>> Hi,
>>
>> I copy the file gmx_xpm2ps from the repository to my gromacs folder
>> /usl/local/gromacs/src/tools (i.e. I substitute the old file by the new
>> one). After that, I run xpm2ps and the problem persisted.
>>
>> Any ideas?
>>
>
> As I said before, you have to actually re-compile and install the git version 
> of
> Gromacs to see any effect.  Further, simply replacing a file likely will not
> work due to a multitude of code changes that have taken place in other source 
> files.
>
>> PS: I run the same job in another i7, but with gromacs version 4.0.7
>> installed, and everything occured well.
>>
>
> Yes, there was a bug introduced in version 4.5.  Please either install the git
> version properly, use xpm2ps included in version 4.0.7, or wait for the 
> release
> of version 4.5.2.
>
> -Justin
>
>> 2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>> Maurício Menegatti Rigo wrote:
>>
>>
>> Hi,
>>
>> Thank you for your answer. Unfortunately, I can't fix my problem.
>> I dont know if I'm doing this right, but first I type the line
>> "/git clone git://git.gromacs.org/gromacs.git
>> 
>> /" in the command line.
>> After all the outputs, I tried to run xpm2ps again, but occured
>> the same error.
>>
>>
>> Simply downloading the source code won't fix the problem.  You have
>> to install (and then use) the resulting binaries.
>>
>> -Justin
>>
>>
>>
>> 2010/10/15 Justin A. Lemkul >  > >>
>>
>>
>>
>>
>>Maurício Menegatti Rigo wrote:
>>
>>Hi,
>>I found the following error when I tried to run xpm2ps.
>>
>>
>>*** glibc detected *** xpm2ps: realloc(): invalid pointer:
>>0x00dd0541 ***
>>=== Backtrace: =
>>/lib/libc.so.6[0x7f20a53b0dd6]
>>/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
>>xpm2ps(save_realloc+0x5e)[0x43741e]
>>xpm2ps[0x42cf24]
>>xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
>>xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
>>xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
>>/lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
>>xpm2ps[0x412949]
>>=== Memory map: 
>>0040-005e3000 r-xp  fc:03 7799252
>>   /usr/local/gromacs/bin/xpm2ps
>>007e2000-007e3000 r-xp 001e2000 fc:03 7799252
>>   /usr/local/gromacs/bin/xpm2ps
>>007e3000-007e9000 rwxp 001e3000 fc:03 7799252
>>   /usr/local/gromacs/bin/xpm2ps
>>007e9000-007ea000 rwxp  00:00 0 00dce000-00def000
>> rwxp
>> 00:00 0  [heap]
>>7f20a5124000-7f20a513a000 r-xp  fc:03 17400029
>>/lib/libgcc_s.so.1
>>7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029
>>/

[gmx-users] Post simulation energy calculation of Ligand - Protein complex

[Rahul ShubhraMandal]

Hi,

I want to calculate the binding energy of ligand-protein complex after
simulation. I am running 10ns simulation, please help me out in this
regards.

Thanks.
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Re: [gmx-users] Post simulation energy calculation of Ligand - Protein complex

[Mark Abraham]

On 17/03/11, Rahul ShubhraMandal   wrote:
> Hi,
> 
> I want to calculate the binding energy of ligand-protein complex after 
> simulation. I am running 10ns simulation, please help me out in this regards.
> 
> 
> Thanks. 
> 
> 

Please start by finding some literature that does something similar to what you 
would like to do. Then think and read about how that might be done in GROMACS. 
Then, please ask a more focussed question :-)

Mark
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