[gmx-users] Re: gmx-users Digest, Vol 83, Issue 63

[Gerrit Groenhof]

 The choice for the QM package depends on what level of QM theory you 
wish to use and what package are available to you. to proceed sue the 
instructions http://wwwuser.gwdg.de/~ggroenh/qmmm.html


Be aware though that QMMM is not to be considered a black box method.

Gerrit



4. QMMM (Haresh)

\

Respected sir,

I am new user in gromacs.
I want to run QMMM on gromacs.
Should I have install all source code like mopac7, guessin,gamess-UK  for QMMM ?

Please help me out.

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[gmx-users] Zero Potential of Mean Force with g_wham

[chris . neale]

g_wham is not the only version of wham. Try using alan grossfield's  
version. Too often, I am afraid, gromacs accessory programs get broken  
in an update (not sure what the general solution is here beyond  
renewed calls for a proper test suite. Perhaps having 20+ programs is  
not ideal for a single software suite where the real focus is only on  
mdrun and grompp?)


Chris.

-- original message --

Hi,

I ran  g_wham 4.5.2 and did get a non-zero PMF curve.
I assume that there is something going on with g_wham on version 4.5.1.

Thank you for your help.

Susana

On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham anu.edu.au>wrote:



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[gmx-users] using one thermostat for entire system ??

[chris . neale]

I'm not sure what the reviewer has in mind. Therefore I would split  
the response into a number of possibilities.


1. If you simulated a box of those solute chemicals in the absence of  
a large solute, and if those solutes do not phase separate, then the  
collisions will equipartition the kinetic energy. The solutes are all  
small and chemically similar insofar as our forcefields treat them.


2. If one then added a large solute, one may be concerned that the  
thermal fluctuations of the solute will partition separately from the  
solute. This is a real concern and this is why I use Langevin dynamics  
(the sd integrator). But you seem to be not very concerned about the  
thermal fluctuations of the solute, so this, on its own, seems to be  
not a concern.


3. The solvent beside a frozen solute: this seems to be a serious  
possibility of a problem. Did you freeze it entirely? If so, does  
gromacs discount this from the kinetic energy? If so, then all seems  
fine. But if you used harmonic restraints then does that somehow suck  
energy out of nearby solvent molecules? I don't know but I might be  
concerned about that if I was trying to draw kinetic conclusions about  
the system.


4. What are your conclusions? Do they even depend on the equipartition  
of energy? If so, how?


So my base answer is that yes, you do possibly have problems and these  
can all be solved with Langevin dynamics (but then kinetics are  
irrelevant and conclusions can not be drawn). But more applicably,  
might these problems affect your conclusions? and here I honestly  
doubt that you have any problem by coupling solvents together. For  
example, if you coupled a box of water together,

 would you expect problems with energy partitioning? I think not.

Finally, to the reviewer's probable question, you have a frozen or  
restrained solute so likely you are not possibly experiencing a frozen  
ice cube type problem. If the reviewer has a particular problem in  
mind, perhaps they would be kind enough to share that with you so that  
you could address it in specific.


Chris.

-- original message --

Thanks Mark for the advice.

I have just rerun a test simulation with each of my gas species
coupled separately to a thermostat and have got similar values for the
quantities of interest (diffusion coefficients). However I am not sure
that this will satisfy the reviewer without a bit more justification
of why I chose to use a single thermostat for my system.

I remembered reading some gromacs information on the application of
thermostats (on which I based my decision to apply one thermostat for
the entire system). I have just managed to locate it on the FAQ page:

http://www.gromacs.org/Documentation/Terminology/Thermostats

What Not To Do
Some hints on practices that generally not a good idea to use:
?   Do not use separate thermostats for every component of your system.
Some molecular dynamics thermostats only work well in the
thermodynamic limit.  A group must be of sufficient size to justify
its own thermostat.  If you use one thermostat for, say, a small
molecule, another for protein, and another for water, you are likely
introducing errors and artifacts that are hard to predict. In
particular, do not couple ions in aqueous solvent in a separate group
from that solvent.

My system consists of
55 molecules of CO2
38 molecules of N2
3 molecules of O2
One large molecule of MCM-41 (mostly frozen but with mobile surface
groups) consisting of 4284 atoms.

My take on this was that the gas molecules were in small supply
compared to the other part of the system so I should avoid using
separate thermostats. Was I mistaken in making this assumption?

Is there any feeling for what "sufficient size" as referred to above
is? Does anyone know of any papers I could reference in my explanation?

Any comments welcome

Thanks

Jenny






Quoting Mark Abraham :


On 8/03/2011 2:50 AM, Jennifer Williams wrote:

Hi,

I simulated the diffusion of small gases (CO2, N2) in a framework   
structure which was mostly frozen with some mobile surface groups.   
I applied a temperature thermostat to the entire system (i.e I   
didn't couple the gas molecules and framework separately). I have   
now been asked the following by a reviewer:


"Please comment on any artefacts that might arise as a result of   
non-equipartition of energies.  For example, what is the calculated  
 temperature of each of the gas species and mobile species?"


I have tried to explore the temperature of each species separately   
but g_energy will only give me the energy of the system as a whole.  
 Are there any other tools within gromacs to look at the  
temperature  of each species in turn from the md runs I already have?


Does anyone have a suggestion as to how I can address the   
reviewer's comment and proove that using one thermostat for the   
whole system is OK (that is what I am hoping!).  Is there anything   
in particular that I should be looking closely at

[gmx-users] spectral density calculation with GROMACS

[ZHANG Lu]

Dear all,
   I am now developing a set of force field parameters and I want to
calculate the spectral density with the normal mode analysis in GROMACS
to check my parameters.
   The point here is that I want to get a plot (spectral density VS
frequencies). Could anybody give me some slides or tutorials so that I
can follow it?
   Thank you in advance.

Best,
Lu

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[gmx-users] QMMM

[Haresh]

Respected sir,

I am new user in gromacs.
I want to run QMMM on gromacs.
Should I have install all source code like mopac7, guessin,gamess-UK  for QMMM ?

Please help me out.


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[gmx-users] RE: heat capacity etc.

[Thomas Koller]

Hello,

i) I use a NPT ensemble and the tool g_energy to extract the heat capacity. 
Nose-Hoover thermostat and Parrinello-Rahman barostat are used. Why do I get 
always c(V)? 

ii) When I use the tool g_energy -vis, I get the thermal compressibility, the 
adiabatic bulk modulus, but not the thermal expansion coefficient. How can I 
get this?

Thomas
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[gmx-users] RE: heat capacity etc.

[Thomas Koller]

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Re: [gmx-users] Treatment of protein termini when there are missing residues

[Mark Abraham]

On 10/03/11, "Justin A. Lemkul"   wrote:
> 
> 
> jo hanna wrote:
> >Hello,
> >
> >My question concerns the 'best' way to treat the terminal groups for a 
> >protein that is missing residues at both termini, e.g. a 530 residue protein 
> >where only residues 15-512 are present in the pdb.
> >
> >My thoughts are that assigning charges to the end groups will result in 
> >areas of charge in regions where there may not be any in the native protein 
> >and could lead
> >to unknown artifacts. Another option would be to 'cap' or add a blocking 
> >group
> >on the end of the protein chain, e.g. ACE, which introduces a group that
> >is non-native to this region of the protein. Or treat the end groups
> >neutrally. I have looked through the literature and while I can find
> >examples of MD being carried out with structures with missing residues at the
> >termini, but I cannot find any description of how these groups are treated.
> >
> >I would appreciate some views on this.
> >
> >N.B. The protein I am wishing to study is catalytically active and therefore 
> >I have confidence that these missing residues have no effect on the activity 
> >of the
> >protein.
> >
> 
> If the termini are unrelated to your goals, you can treat them in almost any 
> way you wish.  Capping is probably the most common.  I would disagree that 
> this is a "non-native" treatment since the capping groups are basically a 
> partial continuation of a normal peptide backbone.
> 

Indeed, and chemically fairly inert by choice. ACE and NME saturate the peptide 
"valence" and add a boring methyl in space that would have been filled with the 
secondary alpha-carbon. Not ideal, but quite good.

Mark
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Re: [gmx-users] heat capacity etc.

[Moeed]

>
>>  From g_energy -h:
>
> Some fluctuation-dependent properties can be calculated provided the
> correct
> energy terms are selected. The following properties will be computed:
> PropertyEnergy terms needed
> ---
> Heat capacity Cp (NPT sims):Enthalpy, Temp
> Heat capacity Cv (NVT sims):Etot, Temp
> Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
> Isothermal compressibility: Vol, Temp
> Adiabatic bulk modulus: Vol, Temp
> ---
>
> Hello,

Thanks for the useful information.

1- Can you please tell me if Etot is the very Upot in the equations stated
in "g_energy -h" and also 'potential' in the list of g_energy terms? I mean
is 'potential"=internal energy?

 2-  To get the enthalpy in NPT run: one needs to substract pv (listed in
g_energy) from 'potential' (in g_energy terms)?

3- Since gromacs gives units in mol of systems, divinding by no. of
molecules (g_energy  -nmol ) should give values per mole of molecules. Now I
am wondering for multicomponent system how -nmol should be set? Say there
are 2 A, 50 B and 1000 C molecules? Is gromcas able to calculate mixture
properties?

I appreciate your help.
Best,
moeed

>
>
>  Regards,
>> Thomas
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] surface tension in gmx

[André Farias de Moura]

regarding your first question, the definition of gamma is not
correct, you are getting energy/length⁴ instead of energy/area
(multiply by Lz instead of dividing by it)


2011/3/9 Pedro Alexandre de Araújo Gomes Lapido Loureiro :
> Hi,
>
>> 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface
>> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e
>> Pres-XX-(bar),  Pres-YY(bar),  Pres--(bar)
>>
>> Can anyone tell me what the difference between these two is?
>
> They should be equal, bearing in mind units conversion.
>
>>
>> 2- In pressure coupling settings there is surface_tension option which I
>> guess is applicable where surface tension needs to be kept fixed. If one
>> want to calculate surface tension I dont think this option make sense. Am I
>> right?
>
> Yes.
>>
>> 3- I am using the following setting: I calculate the average for a 2ns run
>> and different start times as shown below. Although T, P and other quantities
>> are equilibrated after 200ps, surface tension is not giving a constant
>> value. Is that because I am not using berenden P coupling? (As mentioned in
>> the manual surface tension works with berendsen)
>>
>> Pcoupl  =  Parrinello-Rahman
>> Pcoupltype          =  isotropic
>> tau_p   =  1  1
>> compressibility =  4.5e-5
>> ref_p   =  40
>>
>>
>> time period for which average is calculated   Average   RMSD
>> Fluct.  Drift  Tot-Drift
>>
>> ---
>> 1-2000 ps run: #Surf*SurfTen            6.43844    3588.74
>> 3588.35   0.091406    182.721
>> 500-2000 ps    #Surf*SurfTen       12.8518    3605.72
>> 3605.26   0.132126    198.189
>> 1000-2000ps   #Surf*SurfTen        18.8821    3610.97
>> 3610.8    0.11819    118.191
>> 1500-2000ps   #Surf*SurfTen             23.0072    3585.51
>> 3584.93  -0.444037   -222.019
>>
> This question is anything but trivial! Look at the RMSD values compared with
> the averages. The dispersion is so high that you can't be sure if this is or
> not equilibrated.
>
>
>>
>> 4- Assuming I am getting surface tension for a cubic box, to compare this
>> with reported values in literature I need to divide by 6 (no. of surfaces)?
>
> No. You have to divide by the number of interfaces (2 for a bilayer immersed
> in water, for instance)
>
>
>>
>> 5- Does box six affect the results? (mine is 3.3 nm ).
>>
> Yes, but see answer 3, above.
>
>>
>> Thank you,
>>
>>
>>
>>
>>
>>
>>
>>
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>
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Re: [gmx-users] Treatment of protein termini when there are missing residues

[Justin A. Lemkul]

jo hanna wrote:

Hello,

My question concerns the 'best' way to treat the terminal groups for a 
protein that is missing residues at both termini, e.g. a 530 residue 
protein where only residues 15-512 are present in the pdb.


My thoughts are that assigning charges to the end groups will result in 
areas of charge in regions where there may not be any in the native 
protein and could lead
to unknown artifacts. Another option would be to 'cap' or add a blocking 
group

on the end of the protein chain, e.g. ACE, which introduces a group that
is non-native to this region of the protein. Or treat the end groups
neutrally. I have looked through the literature and while I can find
examples of MD being carried out with structures with missing residues 
at the

termini, but I cannot find any description of how these groups are treated.

I would appreciate some views on this.

N.B. The protein I am wishing to study is catalytically active and 
therefore I have confidence that these missing residues have no effect 
on the activity of the

protein.



If the termini are unrelated to your goals, you can treat them in almost any way 
you wish.  Capping is probably the most common.  I would disagree that this is a 
"non-native" treatment since the capping groups are basically a partial 
continuation of a normal peptide backbone.


-Justin


Many thanks,
Jo



--


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] surface tension in gmx

[Pedro Alexandre de Araújo Gomes Lapido Loureiro]

Hi,

 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface
> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e
> Pres-XX-(bar),  Pres-YY(bar),  Pres--(bar)
>
> Can anyone tell me what the difference between these two is?
>
They should be equal, bearing in mind units conversion.


>
> 2- In pressure coupling settings there is surface_tension option which I
> guess is applicable where surface tension needs to be kept fixed. If one
> want to calculate surface tension I dont think this option make sense. Am I
> right?
>
Yes.

>
> 3- I am using the following setting: I calculate the average for a 2ns run
> and different start times as shown below. Although T, P and other quantities
> are equilibrated after 200ps, surface tension is not giving a constant
> value. Is that because I am not using berenden P coupling? (As mentioned in
> the manual surface tension works with berendsen)
>
> Pcoupl  =  Parrinello-Rahman
> Pcoupltype  =  isotropic
> tau_p   =  1  1
> compressibility =  4.5e-5
> ref_p   =  40
>
>
> time period for which average is calculated   Average   RMSD
> Fluct.  Drift  Tot-Drift
>
> ---
> 1-2000 ps run: #Surf*SurfTen6.438443588.74
> 3588.35   0.091406182.721
> 500-2000 ps#Surf*SurfTen   12.85183605.72
> 3605.26   0.132126198.189
> 1000-2000ps   #Surf*SurfTen18.88213610.97
> 3610.80.11819118.191
> 1500-2000ps   #Surf*SurfTen 23.00723585.51
> 3584.93  -0.444037   -222.019
>
> This question is anything but trivial! Look at the RMSD values compared
with the averages. The dispersion is so high that you can't be sure if this
is or not equilibrated.



>
> 4- Assuming I am getting surface tension for a cubic box, to compare this
> with reported values in literature I need to divide by 6 (no. of surfaces)?
>
No. You have to divide by the number of interfaces (2 for a bilayer immersed
in water, for instance)



>
> 5- Does box six affect the results? (mine is 3.3 nm ).
>
> Yes, but see answer 3, above.


>
> Thank you,
>
>
>
>
>
>
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Treatment of protein termini when there are missing residues

[jo hanna]

Hello,

My question concerns the 'best' way to treat the terminal groups for a
protein that is missing residues at both termini, e.g. a 530 residue protein
where only residues 15-512 are present in the pdb.

My thoughts are that assigning charges to the end groups will result in
areas of charge in regions where there may not be any in the native protein
and could lead
to unknown artifacts. Another option would be to 'cap' or add a blocking
group
on the end of the protein chain, e.g. ACE, which introduces a group that
is non-native to this region of the protein. Or treat the end groups
neutrally. I have looked through the literature and while I can find
examples of MD being carried out with structures with missing residues at
the
termini, but I cannot find any description of how these groups are treated.

I would appreciate some views on this.

N.B. The protein I am wishing to study is catalytically active and therefore
I have confidence that these missing residues have no effect on the activity
of the
protein.

Many thanks,
Jo
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Re: [gmx-users] surface tension in gmx

[André Farias de Moura]

if you are interested in the surface tension of a pure liquid, which I assume is
true from your message, then you need to create at least one surface, since
periodic boundary conditions make the model system infinite, i.e., without a
surface whatsoever.

the easiest way to make that happen is to increase the length of the box in
one direction, say the z direction. that way you will end up with a system that
resemble a (thin) liquid film with vacuum below and above, meaning that you
now have two surfaces. run a regular simulation (NVT) e use g_energy to get
the surface tension.

btw: as any other pressure related property, fluctuations are huge.

best

Andre

On Wed, Mar 9, 2011 at 12:25 PM, Elisabeth  wrote:
> Dear gmx users,
>
> Since I am new to surface tension topic I need to ask very trivial
> questions. Please help me out with these simple questions.
>
> As a starting point I am going to calculate surface tension of a pure alkane
> in a cubic box and compare with experimental values.
>
> 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface
> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e
> Pres-XX-(bar),  Pres-YY(bar),  Pres--(bar)
>
> Can anyone tell me what the difference between these two is?
>
> 2- In pressure coupling settings there is surface_tension option which I
> guess is applicable where surface tension needs to be kept fixed. If one
> want to calculate surface tension I dont think this option make sense. Am I
> right?
>
> 3- I am using the following setting: I calculate the average for a 2ns run
> and different start times as shown below. Although T, P and other quantities
> are equilibrated after 200ps, surface tension is not giving a constant
> value. Is that because I am not using berenden P coupling? (As mentioned in
> the manual surface tension works with berendsen)
>
> Pcoupl  =  Parrinello-Rahman
> Pcoupltype          =  isotropic
> tau_p   =  1  1
> compressibility =  4.5e-5
> ref_p   =  40
>
>
> time period for which average is calculated   Average   RMSD
> Fluct.  Drift  Tot-Drift
> ---
> 1-2000 ps run: #Surf*SurfTen            6.43844    3588.74
> 3588.35   0.091406    182.721
> 500-2000 ps    #Surf*SurfTen       12.8518    3605.72
> 3605.26   0.132126    198.189
> 1000-2000ps   #Surf*SurfTen        18.8821    3610.97
> 3610.8    0.11819    118.191
> 1500-2000ps   #Surf*SurfTen             23.0072    3585.51
> 3584.93  -0.444037   -222.019
>
>
>
> 4- Assuming I am getting surface tension for a cubic box, to compare this
> with reported values in literature I need to divide by 6 (no. of surfaces)?
>
> 5- Does box six affect the results? (mine is 3.3 nm ).
>
>
> Thank you,
>
>
>
>
>
>
>
>
> --
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Re: [gmx-users] heat capacity etc.

[David van der Spoel]

On 2011-03-09 19.48, Thomas Koller wrote:

Hello,

I want to calculate the isobaric heat capacity, the thermal expansion 
coefficient and the isothermal compressibility:

i) My value for the heat capacity (NPT) is very low. I used option -nmol. Whan 
can be the reason or is the calculation of this property not accurate with this 
tool? By the way, why is there always written c(v) although I analyze a NPT run 
c(P)?


Did you use a thermostat that yields a canonical ensemble?
The best way to compute the Cp is from the fluctuations in the enthalpy.
Note that the quantum corrections / constraint corrections are not 
correct. We are working on a better method.

ii) How can I obtain the thermal expansion coefficient from the NPT run, I 
can't see it? The isothermal compressibility is calculated.


From g_energy -h:

Some fluctuation-dependent properties can be calculated provided the correct
energy terms are selected. The following properties will be computed:
PropertyEnergy terms needed
---
Heat capacity Cp (NPT sims):Enthalpy, Temp
Heat capacity Cv (NVT sims):Etot, Temp
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility: Vol, Temp
Adiabatic bulk modulus: Vol, Temp
---




Regards,
Thomas



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Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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[gmx-users] heat capacity etc.

[Thomas Koller]

Hello,

I want to calculate the isobaric heat capacity, the thermal expansion 
coefficient and the isothermal compressibility:

i) My value for the heat capacity (NPT) is very low. I used option -nmol. Whan 
can be the reason or is the calculation of this property not accurate with this 
tool? By the way, why is there always written c(v) although I analyze a NPT run 
c(P)?

ii) How can I obtain the thermal expansion coefficient from the NPT run, I 
can't see it? The isothermal compressibility is calculated.

Regards,
Thomas
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Re: [gmx-users] Zero Potential of Mean Force with g_wham

[Susana Tomasio]

Hi,

I ran  g_wham 4.5.2 and did get a non-zero PMF curve.
I assume that there is something going on with g_wham on version 4.5.1.

Thank you for your help.

Susana

On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham wrote:

>  On 10/03/2011 1:43 AM, Susana Tomasio wrote:
>
> Thank you Jianguo.
>
> So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1?
>
>
> Quite likely. Check the change logs on the GROMCACS website for relevant
> issues.
>
> Mark
>
>
>
> Best regards,
>
> Susana
>
>
>
> On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li  wrote:
>
>>  I met the same problem when using 4.5.1 for some systems, the PMF shows
>> zero curve, while the hist file looks fine. The problem disappears when
>> using 4.5.2.
>> Jianguo
>>
>>  --
>> *From:* Susana Tomasio 
>> *To:* gmx-users@gromacs.org
>> *Sent:* Wednesday, 9 March 2011 20:07:25
>> *Subject:* [gmx-users] Zero Potential of Mean Force with g_wham
>>
>> Dear all,
>>
>> I am running umbrella sampling of a molecule through a lipid bilayer with
>> gromacs 4.5.1.
>> When I extracted the potential of mean force with g_wham I got zero for
>> all the windows.
>> Any ideas of why this is happening?
>>
>> This is the command I used:
>> g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist
>>
>> And this is the pull code of my .mdp file:
>>
>> ; Pull code
>> pull=  umbrella
>> pull_geometry   =  position
>> pull_dim=  N N Y
>> pull_start  =  yes
>> pull_ngroups=  1
>> pull_group0 =  Bilayer
>> pull_group1 =  Protein
>> pull_vec1   =  0 0 0
>> pull_init1  =  0 0 0
>> pull_rate1  =  0
>> pull_pbcatom0   =  1453
>> pull_pbcatom1   =  13187
>> pull_k1 =  3000 ;  kJ mol^-1 nm^-2
>> pull_nstxout=  1000 ; every 2 ps
>> pull_nstfout=  1000 ; every 2 ps
>>
>> Thank you.
>> Best regards,
>>
>> Susana
>>
>>
>> --
>> 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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>>
>
>
>
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[gmx-users] surface tension in gmx

[Elisabeth]

Dear gmx users,

Since I am new to surface tension topic I need to ask very trivial
questions. Please help me out with these simple questions.

As a starting point I am going to calculate surface tension of a pure alkane
in a cubic box and compare with experimental values.

1- g_energy is giving #Surf*SurfTen by default. On the other hand surface
tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e
Pres-XX-(bar),  Pres-YY(bar),  Pres--(bar)

Can anyone tell me what the difference between these two is?

2- In pressure coupling settings there is surface_tension option which I
guess is applicable where surface tension needs to be kept fixed. If one
want to calculate surface tension I dont think this option make sense. Am I
right?

3- I am using the following setting: I calculate the average for a 2ns run
and different start times as shown below. Although T, P and other quantities
are equilibrated after 200ps, surface tension is not giving a constant
value. Is that because I am not using berenden P coupling? (As mentioned in
the manual surface tension works with berendsen)

Pcoupl  =  Parrinello-Rahman
Pcoupltype  =  isotropic
tau_p   =  1  1
compressibility =  4.5e-5
ref_p   =  40


time period for which average is calculated   Average   RMSD
Fluct.  Drift  Tot-Drift
---
1-2000 ps run: #Surf*SurfTen6.438443588.74
3588.35   0.091406182.721
500-2000 ps#Surf*SurfTen   12.85183605.72
3605.26   0.132126198.189
1000-2000ps   #Surf*SurfTen18.88213610.97
3610.80.11819118.191
1500-2000ps   #Surf*SurfTen 23.00723585.51
3584.93  -0.444037   -222.019



4- Assuming I am getting surface tension for a cubic box, to compare this
with reported values in literature I need to divide by 6 (no. of surfaces)?

5- Does box six affect the results? (mine is 3.3 nm ).


Thank you,
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Re: [gmx-users] Zero Potential of Mean Force with g_wham

[Mark Abraham]

On 10/03/2011 1:43 AM, Susana Tomasio wrote:

Thank you Jianguo.

So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1?


Quite likely. Check the change logs on the GROMCACS website for relevant 
issues.


Mark



Best regards,

Susana



On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li > wrote:


I met the same problem when using 4.5.1 for some systems, the PMF
shows zero curve, while the hist file looks fine. The problem
disappears when using 4.5.2.
Jianguo


*From:* Susana Tomasio mailto:susietoma...@gmail.com>>
*To:* gmx-users@gromacs.org 
*Sent:* Wednesday, 9 March 2011 20:07:25
*Subject:* [gmx-users] Zero Potential of Mean Force with g_wham

Dear all,

I am running umbrella sampling of a molecule through a lipid
bilayer with gromacs 4.5.1.
When I extracted the potential of mean force with g_wham I got
zero for all the windows.
Any ideas of why this is happening?

This is the command I used:
g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist

And this is the pull code of my .mdp file:

; Pull code
pull=  umbrella
pull_geometry   =  position
pull_dim=  N N Y
pull_start  =  yes
pull_ngroups=  1
pull_group0 =  Bilayer
pull_group1 =  Protein
pull_vec1   =  0 0 0
pull_init1  =  0 0 0
pull_rate1  =  0
pull_pbcatom0   =  1453
pull_pbcatom1   =  13187
pull_k1 =  3000 ;  kJ mol^-1 nm^-2
pull_nstxout=  1000 ; every 2 ps
pull_nstfout=  1000 ; every 2 ps

Thank you.
Best regards,

Susana


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Re: [gmx-users] secondary structure propensities of residues

[Mark Abraham]

On 10/03/2011 1:36 AM, Justin A. Lemkul wrote:



ZHAO Lina wrote:

Hi,

How do get the percentage of the secondary structure propensities of 
residues?


seems dssp none such effect?



The scout.xvg file contains everything you need (in a broad sense) - 
number of residues in a given secondary structure over time.  If you 
need a per-residue breakdown, there is no Gromacs tool that does that, 
but the .xpm file contains that information, so you can write your own 
script and extract it.


Actually I modified do_dssp in late January to do that. The OP will need 
to download the release-4-5-patches version of src/tools/do_dssp.c and 
copy it to their normal installation directory (or compile 
release-4-5-patches).


Mark
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Re: [gmx-users] Problem when running in many nodes

[Justin A. Lemkul]

Tomy van Batis wrote:

Dear all

The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I 
experience some difficulties when running in parallel.


Initially, my simulation box has dimensions :

* 3.30507   2.67145  41.15800*

and it consists of 25 polymers chains with 50 beads/chain

When I run NVT using 8 or 16 cores, everything is working fine, but when 
I compress it to dimensions:


*3.30507   2.67145  10.64441*

and try again to run NVT in 8 cores, I have the following error message:

/There is no domain decomposition for 8 nodes that is compatible with 
the given box and a minimum cell size of 2.5 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS 
settings/


As I saw this is well known error, but I can't understand how to fix it :-)



A nearly identical case was posted just a few days ago, and reasons for the 
error discussed:


http://lists.gromacs.org/pipermail/gmx-users/2011-March/059063.html

with a possible work-around:

http://lists.gromacs.org/pipermail/gmx-users/2011-March/059079.html

 From what I understood, this is happening because_* I use constrains in 
all the bonds of my system*_




Constraints are but one of many considerations in establishing DD cells.

-Justin


In my .log file I see the following:

/Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 0.000 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 2.000 nm
Estimated maximum distance required for P-LINCS: 2.000 nm
This distance will limit the DD cell size, you can override this with -rcon
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 2.500 nm
The maximum allowed number of cells is: X 1 Y 1 Z 4/

, but I can't understand how to use -rcon or -dds in order to fix my problem

Any suggestions?

Thanks in advance
Chrysostomos









--


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] Problem when running in many nodes

[Tomy van Batis]

Dear all

The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I
experience some difficulties when running in parallel.

Initially, my simulation box has dimensions :

* 3.30507   2.67145  41.15800*

and it consists of 25 polymers chains with 50 beads/chain

When I run NVT using 8 or 16 cores, everything is working fine, but when I
compress it to dimensions:

*3.30507   2.67145  10.64441*

and try again to run NVT in 8 cores, I have the following error message:

*There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 2.5 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings*

As I saw this is well known error, but I can't understand how to fix it :-)

>From what I understood, this is happening because* I use constrains in all
the bonds of my system*

In my .log file I see the following:

*Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 0.000 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 2.000 nm
Estimated maximum distance required for P-LINCS: 2.000 nm
This distance will limit the DD cell size, you can override this with -rcon
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 2.500 nm
The maximum allowed number of cells is: X 1 Y 1 Z 4*

, but I can't understand how to use -rcon or -dds in order to fix my problem

Any suggestions?

Thanks in advance
Chrysostomos
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Re: [gmx-users] Zero Potential of Mean Force with g_wham

[Susana Tomasio]

Thank you Jianguo.

So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1?

Best regards,

Susana



On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li  wrote:

> I met the same problem when using 4.5.1 for some systems, the PMF shows
> zero curve, while the hist file looks fine. The problem disappears when
> using 4.5.2.
> Jianguo
>
>  --
> *From:* Susana Tomasio 
> *To:* gmx-users@gromacs.org
> *Sent:* Wednesday, 9 March 2011 20:07:25
> *Subject:* [gmx-users] Zero Potential of Mean Force with g_wham
>
> Dear all,
>
> I am running umbrella sampling of a molecule through a lipid bilayer with
> gromacs 4.5.1.
> When I extracted the potential of mean force with g_wham I got zero for all
> the windows.
> Any ideas of why this is happening?
>
> This is the command I used:
> g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist
>
> And this is the pull code of my .mdp file:
>
> ; Pull code
> pull=  umbrella
> pull_geometry   =  position
> pull_dim=  N N Y
> pull_start  =  yes
> pull_ngroups=  1
> pull_group0 =  Bilayer
> pull_group1 =  Protein
> pull_vec1   =  0 0 0
> pull_init1  =  0 0 0
> pull_rate1  =  0
> pull_pbcatom0   =  1453
> pull_pbcatom1   =  13187
> pull_k1 =  3000 ;  kJ mol^-1 nm^-2
> pull_nstxout=  1000 ; every 2 ps
> pull_nstfout=  1000 ; every 2 ps
>
> Thank you.
> Best regards,
>
> Susana
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] secondary structure propensities of residues

[Justin A. Lemkul]

ZHAO Lina wrote:

Hi,

How do get the percentage of the secondary structure propensities of 
residues?


seems dssp none such effect?



The scout.xvg file contains everything you need (in a broad sense) - number of 
residues in a given secondary structure over time.  If you need a per-residue 
breakdown, there is no Gromacs tool that does that, but the .xpm file contains 
that information, so you can write your own script and extract it.


-Justin


Thanks for any answers.

lina




--


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


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Re: [gmx-users] Zero Potential of Mean Force with g_wham

[Jianguo Li]

I met the same problem when using 4.5.1 for some systems, the PMF shows zero 
curve, while the hist file looks fine. The problem disappears when using 4.5.2.
Jianguo





From: Susana Tomasio 
To: gmx-users@gromacs.org
Sent: Wednesday, 9 March 2011 20:07:25
Subject: [gmx-users] Zero Potential of Mean Force with g_wham

Dear all,

I am running umbrella sampling of a molecule through a lipid bilayer with 
gromacs 4.5.1.
When I extracted the potential of mean force with g_wham I got zero for all the 
windows.
Any ideas of why this is happening?

This is the command I used: 
g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist

And this is the pull code of my .mdp file:

; Pull code
pull    =  umbrella 
pull_geometry   =  position 
pull_dim    =  N N Y    
pull_start  =  yes  
pull_ngroups    =  1  
pull_group0 =  Bilayer 
pull_group1 =  Protein    
pull_vec1   =  0 0 0    
pull_init1  =  0 0 0   
pull_rate1  =  0   
pull_pbcatom0   =  1453   
pull_pbcatom1   =  13187   
pull_k1 =  3000 ;  kJ mol^-1 nm^-2
pull_nstxout    =  1000 ; every 2 ps
pull_nstfout    =  1000 ; every 2 ps

Thank you.
Best regards,

Susana


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[gmx-users] secondary structure propensities of residues

[ZHAO Lina]

Hi,

How do get the percentage of the secondary structure propensities of
residues?

seems dssp none such effect?

Thanks for any answers.

lina
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Re: [gmx-users] Definition of helicity

[Justin A. Lemkul]

cd...@ipc.uni-karlsruhe.de wrote:
> Hi Justin,
> 
> Thank you for your notice.
> I am afraid my explanation was not enough.
> When protein atoms is specified, g_helix seems to calculate the 
> helicities for all residue.
> And then, the helicity value of each residues is written into helicity.xvg.
> The value probably means how much percentage of time does each residue 
> form alpha-helix.
> I would like to know how does it judge the alpha-helix? What is the 
> criterion?
> 

That is too broad of a question to get a useful answer.  Only you know your
intents.  What is it that you're looking to evaluate?  I don't know how one
generically judges an alpha helix aside from its basic geometry.  You'll have to
explain your goals very precisely if you want any more useful help.

-Justin

> Hiroshi
> 
> Quoting "Justin A. Lemkul" :
> 
>>
>>
>> cd...@ipc.uni-karlsruhe.de wrote:
>>> Dear all,
>>>
>>> Now I am using g_helix module to calculate helicity of each residues in
>>> protein.
>>> In the manual, there seems to be no detailed description about the
>>> definition of the helicity.
>>> Could you let me know the detail, or where should I refer to.
>>>
>>
>> As implied by the rise and ellipticity information in the g_helix 
>> description,
>> it would seem that an ideal helix is an alpha helix.  I doubt this 
>> tool is
>> useful when analyzing single residues; the program determines the longest
>> continuous alpha helix and calculates properties related to it.  
>> g_helix may
>> work on a single residue, but if you get output of all zeroes, don't be
>> surprised.  do_dssp may also be useful.
>>
>> -Justin
>>
>>> Thank you in advance,
>>>
>>> Hiroshi
>>> 
>>> Hiroshi Watanabe
>>> Karlsruhe University
>>> E-mail: hiroshi.watan...@chemie.uni-karlsruhe.de
>>>
>>>
>>
>> -- 
>> 
>>
>> 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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>>
> 
> 

-- 


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] Definition of helicity

[Mark Abraham]

On 10/03/2011 12:58 AM, cd...@ipc.uni-karlsruhe.de wrote:
> Hi Justin,
>
> Thank you for your notice.
> I am afraid my explanation was not enough.
> When protein atoms is specified, g_helix seems to calculate the
> helicities for all residue.
> And then, the helicity value of each residues is written into
> helicity.xvg.
> The value probably means how much percentage of time does each residue
> form alpha-helix.
> I would like to know how does it judge the alpha-helix? What is the
> criterion?

If g_helix -h doesn't help you, then you'll have to read the code for
the details of what criterion it is using. Presumably src/tools/gmx_helix.c

Mark

>
> Hiroshi
>
> Quoting "Justin A. Lemkul" :
>
>>
>>
>> cd...@ipc.uni-karlsruhe.de wrote:
>>> Dear all,
>>>
>>> Now I am using g_helix module to calculate helicity of each residues in
>>> protein.
>>> In the manual, there seems to be no detailed description about the
>>> definition of the helicity.
>>> Could you let me know the detail, or where should I refer to.
>>>
>>
>> As implied by the rise and ellipticity information in the g_helix
>> description,
>> it would seem that an ideal helix is an alpha helix. I doubt this
>> tool is
>> useful when analyzing single residues; the program determines the
>> longest
>> continuous alpha helix and calculates properties related to it.
>> g_helix may
>> work on a single residue, but if you get output of all zeroes, don't be
>> surprised. do_dssp may also be useful.
>>
>> -Justin
>>
>>> Thank you in advance,
>>>
>>> Hiroshi
>>> 
>>> Hiroshi Watanabe
>>> Karlsruhe University
>>> E-mail: hiroshi.watan...@chemie.uni-karlsruhe.de
>>>
>>>
>>
>> -- 
>> 
>>
>> 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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>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
>
>

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Re: [gmx-users] Definition of helicity

[cd231]

Hi Justin,

Thank you for your notice.
I am afraid my explanation was not enough.
When protein atoms is specified, g_helix seems to calculate the 
helicities for all residue.

And then, the helicity value of each residues is written into helicity.xvg.
The value probably means how much percentage of time does each residue 
form alpha-helix.

I would like to know how does it judge the alpha-helix? What is the criterion?

Hiroshi

Quoting "Justin A. Lemkul" :




cd...@ipc.uni-karlsruhe.de wrote:

Dear all,

Now I am using g_helix module to calculate helicity of each residues in
protein.
In the manual, there seems to be no detailed description about the
definition of the helicity.
Could you let me know the detail, or where should I refer to.



As implied by the rise and ellipticity information in the g_helix 
description,

it would seem that an ideal helix is an alpha helix.  I doubt this tool is
useful when analyzing single residues; the program determines the longest
continuous alpha helix and calculates properties related to it.  g_helix may
work on a single residue, but if you get output of all zeroes, don't be
surprised.  do_dssp may also be useful.

-Justin


Thank you in advance,

Hiroshi

Hiroshi Watanabe
Karlsruhe University
E-mail: hiroshi.watan...@chemie.uni-karlsruhe.de




--


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] Instantaneous Square Displacement

[Jennifer Williams]

Thanks for the advice. I has also found that last source on google and  
have been thinking how I could apply this.


I assume that if I plotted [rt - r0]^2 against time then (for a single  
molecule) I would get peaks on the graph when the molecules are mobile  
and dips (where [rt-r0]^2 is close to zero) for the periods where  
molecules are stuck.


This would seem to make sense only for a single molecule (as Mark  
suggested) as averaged over all molecules, the peaks and troughs would  
average out and I wouldn't really be illustrating anything.


I have made a rough sketch of what the plot should look like and for a  
few moves of the molecules (using only 15 positions) it seems to make  
sense. However I don't really find it intuitive given that iSD isn't  
widely used and for more than a few moves it gets crowded and  
difficult to interpret.


So as I see it, the graph would sample only one molecule over a short  
time period.


Any more thoughts on this?

Thanks

Jenny

Quoting "Justin A. Lemkul" :




Mark Abraham wrote:

On 8/03/2011 3:01 AM, Jennifer Williams wrote:


Hi,

I am writing a paper where I describe that gas molecules move  
inside a pore and then stick for long periods of time in  
occlusions in the pore wall.


A reviewer has mentioned that I could illustrate this effect by  
using "instantaneous square-displacement".


I have already produced MSD vs time plots and used them to obtain  
the self diffusion coefficient. Can someone shed some light on how  
I can obtain the instantaneous square displacement in gromacs?


I have no idea what "ISD" means, and Google doesn't know either :)  
Perhaps they want to see the diffusion of a single molecule?




Searching for "instantaneous square displacement" turns up very  
little (3 results), but the last seems to be what you need, as long  
as this person is correct:


http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1

Section 2.3.3.

-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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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861


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Re: [gmx-users] using one thermostat for entire system ??

[Jennifer Williams]

Thanks Mark for the advice.

I have just rerun a test simulation with each of my gas species  
coupled separately to a thermostat and have got similar values for the  
quantities of interest (diffusion coefficients). However I am not sure  
that this will satisfy the reviewer without a bit more justification  
of why I chose to use a single thermostat for my system.


I remembered reading some gromacs information on the application of  
thermostats (on which I based my decision to apply one thermostat for  
the entire system). I have just managed to locate it on the FAQ page:


http://www.gromacs.org/Documentation/Terminology/Thermostats

What Not To Do
Some hints on practices that generally not a good idea to use:
?	Do not use separate thermostats for every component of your system.  
Some molecular dynamics thermostats only work well in the  
thermodynamic limit.  A group must be of sufficient size to justify  
its own thermostat.  If you use one thermostat for, say, a small  
molecule, another for protein, and another for water, you are likely  
introducing errors and artifacts that are hard to predict. In  
particular, do not couple ions in aqueous solvent in a separate group  
from that solvent.


My system consists of
55 molecules of CO2
38 molecules of N2
3 molecules of O2
One large molecule of MCM-41 (mostly frozen but with mobile surface  
groups) consisting of 4284 atoms.


My take on this was that the gas molecules were in small supply  
compared to the other part of the system so I should avoid using  
separate thermostats. Was I mistaken in making this assumption?


Is there any feeling for what "sufficient size" as referred to above  
is? Does anyone know of any papers I could reference in my explanation?


Any comments welcome

Thanks

Jenny






Quoting Mark Abraham :


On 8/03/2011 2:50 AM, Jennifer Williams wrote:

Hi,

I simulated the diffusion of small gases (CO2, N2) in a framework  
structure which was mostly frozen with some mobile surface groups.  
I applied a temperature thermostat to the entire system (i.e I  
didn't couple the gas molecules and framework separately). I have  
now been asked the following by a reviewer:


"Please comment on any artefacts that might arise as a result of  
non-equipartition of energies.  For example, what is the calculated  
temperature of each of the gas species and mobile species?"


I have tried to explore the temperature of each species separately  
but g_energy will only give me the energy of the system as a whole.  
Are there any other tools within gromacs to look at the temperature  
of each species in turn from the md runs I already have?


Does anyone have a suggestion as to how I can address the  
reviewer's comment and proove that using one thermostat for the  
whole system is OK (that is what I am hoping!).  Is there anything  
in particular that I should be looking closely at?


g_energy can only report the global temperature as saved in the .edr  
file, computed during the simulation. The only way of decomposing  
the temperature is to save velocities to the .trr file with nstvout.  
(Some colleagues had to do this recently.) Then, judicious use of  
trjconv to take subsets and matching topology hacking (tpbconv  
doesn't quite work) mean you can use mdrun -rerun on the subset .trr  
and matching .tpr to get a group-wise temperature. That can  
demonstrate whether temperature differentials (ie. heat flows) exist.


If you didn't save velocities, you're out of luck.

Mark
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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861


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[gmx-users] Re: 4. Re: QMMM (Txema Mercero)

[Gerrit Groenhof]

 Please be more specific than not successful.

And also please understand that there are two things involved: the 
installation, which is so complicated because the gaussian license 
forbids distrubution of source code.


The actual QM, which sometimes is not thought through well enough. A 
general advice therefore is to first try to see if you can do the QM on 
the isolated (sub) system with a default QM package.


Since the interface with Orca runs and installs more smoothly, I suggest 
try that.


Hope this helps,

Gerrit



4. Re: QMMM (Txema Mercero)


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Re: [gmx-users] Definition of helicity

[Justin A. Lemkul]

cd...@ipc.uni-karlsruhe.de wrote:
> Dear all,
> 
> Now I am using g_helix module to calculate helicity of each residues in 
> protein.
> In the manual, there seems to be no detailed description about the 
> definition of the helicity.
> Could you let me know the detail, or where should I refer to.
> 

As implied by the rise and ellipticity information in the g_helix description,
it would seem that an ideal helix is an alpha helix.  I doubt this tool is
useful when analyzing single residues; the program determines the longest
continuous alpha helix and calculates properties related to it.  g_helix may
work on a single residue, but if you get output of all zeroes, don't be
surprised.  do_dssp may also be useful.

-Justin

> Thank you in advance,
> 
> Hiroshi
> 
> Hiroshi Watanabe
> Karlsruhe University
> E-mail: hiroshi.watan...@chemie.uni-karlsruhe.de
> 
> 

-- 


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] Density of water, Dispcorr and rmsd

[Mark Abraham]

On 9/03/2011 10:43 PM, Kavyashree M wrote:

Dear users,

What is the difference between densities predicted by tip4p and 
spc models?
I am using tip4p (with OPLSAA forcefield) in the simulation, during 
position restrained
dynamics, Average water density is around 1015kg-m-3 at 300K which is 
quite far from

expt value..


You're modelling a flexible three-atom two-lone-pair fluid that does 
proton transfer and hydrogen bonding with a non-dissociative rigid 
four-point three-parameter model. 1.5% error starts to sound OK 
actually. If you were actually using position restraints on those water 
molecules, then all you are observing is the density of the starting 
configuration. Anyway, deviations of up to about 20-30 are expected, and 
the size and sign depend on your pressure coupling scheme, the water 
model, and what the water model was parametrized to reproduce.




The Dispersion correction (DIspCorr) is applicable only when we 
use vdw_type = cut off?

Any known disadvantage of using vdw_type = switch?


Please do your homework reading the (for example) the manual and primary 
literature, as suitable.


What could be the possible reasons for getting quite noisy and not 
equilibrating RMSD

of backbone  during MD simulations?


Non-ergodicity of finite simulations, a broken model, an intrinsically 
unstable system, wrong observations, periodicity artefacts, lack of 
experience in judging how significant noise is... anything really :-)


Mark
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Re: [gmx-users] creating a bilayer of dppc

[Justin A. Lemkul]

Igor Marques wrote:

dear delara,

converting the monolayer gro to pdb with editconf and then using that 
pdb in packmol might be a way of doing it.


don't forget to adjust your *top file to the new number of items (2x)  
and their order.


that should do it, i guess



That might work, or simply:

1. Rotate the existing monolayer by 180 and translate suitably with editconf
2. Position both monolayers in a box (also editconf)
3. Concatenate the two coordinate files.

-Justin



best regards,
igor




  Igor Marques
  http://molecular-modeling.dq.ua.pt/


On Wed, Mar 9, 2011 at 11:16 AM, delara aghaie > wrote:


*Dear gromacs users*
*having the .gro file for the dppc monolayer, how can i create a
bilayer?*
*I am interested in making bilayer from the equilibrated monolayer
which i have for dppc.*
*what changes are necessary to be done in simulation files to start
a run with the bilayer?*
*Thanks for your time*
*D.M
*
--- On *Tue, 3/8/11, Justin A. Lemkul /mailto:jalem...@vt.edu>>/* wrote:


From: Justin A. Lemkul mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Instantaneous Square Displacement
To: "Discussion list for GROMACS users" mailto:gmx-users@gromacs.org>>
Date: Tuesday, March 8, 2011, 2:57 PM



Mark Abraham wrote:
 > On 8/03/2011 3:01 AM, Jennifer Williams wrote:
 >>
 >> Hi,
 >>
 >> I am writing a paper where I describe that gas molecules
move inside a pore and then stick for long periods of time in
occlusions in the pore wall.
 >>
 >> A reviewer has mentioned that I could illustrate this effect
by using "instantaneous square-displacement".
 >>
 >> I have already produced MSD vs time plots and used them to
obtain the self diffusion coefficient. Can someone shed some
light on how I can obtain the instantaneous square displacement
in gromacs?
 >
 > I have no idea what "ISD" means, and Google doesn't know
either :) Perhaps they want to see the diffusion of a single
molecule?
 >

Searching for "instantaneous square displacement" turns up very
little (3 results), but the last seems to be what you need, as
long as this person is correct:


http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1

Section 2.3.3.

-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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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] Zero Potential of Mean Force with g_wham

[Susana Tomasio]

Dear all,

I am running umbrella sampling of a molecule through a lipid bilayer with
gromacs 4.5.1.
When I extracted the potential of mean force with g_wham I got zero for all
the windows.
Any ideas of why this is happening?

This is the command I used:
g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist

And this is the pull code of my .mdp file:

; Pull code
pull=  umbrella
pull_geometry   =  position
pull_dim=  N N Y
pull_start  =  yes
pull_ngroups=  1
pull_group0 =  Bilayer
pull_group1 =  Protein
pull_vec1   =  0 0 0
pull_init1  =  0 0 0
pull_rate1  =  0
pull_pbcatom0   =  1453
pull_pbcatom1   =  13187
pull_k1 =  3000 ;  kJ mol^-1 nm^-2
pull_nstxout=  1000 ; every 2 ps
pull_nstfout=  1000 ; every 2 ps

Thank you.
Best regards,

Susana
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[gmx-users] Definition of helicity

[cd231]

Dear all,

Now I am using g_helix module to calculate helicity of each residues in 
protein.
In the manual, there seems to be no detailed description about the 
definition of the helicity.

Could you let me know the detail, or where should I refer to.

Thank you in advance,

Hiroshi

Hiroshi Watanabe
Karlsruhe University
E-mail: hiroshi.watan...@chemie.uni-karlsruhe.de


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Re: [gmx-users] g_rms and g_cluster

[Mark Abraham]

On 09/03/11, shahid nayeem   wrote:
> Hi Justin
> If I make an index group with backbone and CA C N O group of the
> concerned residues and then do least square fitting then do this
> fitting is equivalent to backbone fitting first and then translating
> to coincide CA of the residue of interest. Is there any other
> programme developed for gromacs trajectory analysis where I can do
> backbone fitting first and then translate to coincide CA of residue of
> interest before calculating RMSD.
> 

Group-wise fitting subject to the constraint of particular atoms overlaid 
requires a quite different algorithm from plain group-wise fitting, and is not 
implemented. You can do the plain fit, calculate the relative displacement of 
one CA from another by hand, and do the corresponding translation with 
editconf, but I doubt you're going to learn anything...

Mark


> 
> Shahid Nayeem
> 
> On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul  wrote:
> >
> >
> > shahid nayeem wrote:
> >>
> >> Dear All
> >>
> >> I want to calculate RMSD of one side chain residue from simulation
> >> trajectory after full backbone alignment as well as translating to
> >> coincide CA of the residue of interest. Is it possible to do with
> >> g_rms both backbone alignment as well as translating to coincide CA.
> >
> > Least-squares fitting is performed on whatever group you choose (i.e.
> > backbone), and the calculation group can then be whatever you want.  You can
> > use trjconv to do translational fitting, but I don't know that you can force
> > g_rms to always align this certain atom and still perform a backbone fit;
> > these two may work against one another, even if the difference is small.
> >
> >> Another clarification is that in gromacs g_cluster how can I use
> >> greedy algorithm for clustering.
> >
> > What is a "greedy" algorithm?  The available methods are described in the
> > manual and/or g_cluster -h.
> >
> > -Justin
> >
> >> Shahid Nayeem
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Density of water, Dispcorr and rmsd

[Kavyashree M]

Dear users,

What is the difference between densities predicted by tip4p and spc
models?
I am using tip4p (with OPLSAA forcefield) in the simulation, during position
restrained
dynamics, Average water density is around 1015kg-m-3 at 300K which is quite
far from
expt value..

The Dispersion correction (DIspCorr) is applicable only when we use
vdw_type = cut off?
Any known disadvantage of using vdw_type = switch?

What could be the possible reasons for getting quite noisy and not
equilibrating RMSD
of backbone  during MD simulations?

Thanking you
With Regards
M. Kavyashree
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Re: [gmx-users] creating a bilayer of dppc

[Igor Marques]

dear delara,

converting the monolayer gro to pdb with editconf and then using that pdb in
packmol might be a way of doing it.

don't forget to adjust your *top file to the new number of items (2x)  and
their order.

that should do it, i guess


best regards,
igor




  Igor Marques
  http://molecular-modeling.dq.ua.pt/


On Wed, Mar 9, 2011 at 11:16 AM, delara aghaie  wrote:

> *Dear gromacs users*
> *having the .gro file for the dppc monolayer, how can i create a bilayer?*
> *I am interested in making bilayer from the equilibrated monolayer which i
> have for dppc.*
> *what changes are necessary to be done in simulation files to start a run
> with the bilayer?*
> *Thanks for your time*
> *D.M
> *
> --- On *Tue, 3/8/11, Justin A. Lemkul * wrote:
>
>
> From: Justin A. Lemkul 
> Subject: Re: [gmx-users] Instantaneous Square Displacement
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, March 8, 2011, 2:57 PM
>
>
>
> Mark Abraham wrote:
> > On 8/03/2011 3:01 AM, Jennifer Williams wrote:
> >>
> >> Hi,
> >>
> >> I am writing a paper where I describe that gas molecules move inside a
> pore and then stick for long periods of time in occlusions in the pore wall.
> >>
> >> A reviewer has mentioned that I could illustrate this effect by using
> "instantaneous square-displacement".
> >>
> >> I have already produced MSD vs time plots and used them to obtain the
> self diffusion coefficient. Can someone shed some light on how I can obtain
> the instantaneous square displacement in gromacs?
> >
> > I have no idea what "ISD" means, and Google doesn't know either :)
> Perhaps they want to see the diffusion of a single molecule?
> >
>
> Searching for "instantaneous square displacement" turns up very little (3
> results), but the last seems to be what you need, as long as this person is
> correct:
>
>
> http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1
>
> Section 2.3.3.
>
> -Justin
>
> -- 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> -- gmx-users mailing list
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> .
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>
>
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[gmx-users] membrane protein

[mohsen ramezanpour]

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] creating a bilayer of dppc

[delara aghaie]

Dear gromacs users
having the .gro file for the dppc monolayer, how can i create a bilayer?
I am interested in making bilayer from the equilibrated monolayer which i have 
for dppc.
what changes are necessary to be done in simulation files to start a run with 
the bilayer?
Thanks for your time
D.M

--- On Tue, 3/8/11, Justin A. Lemkul  wrote:


From: Justin A. Lemkul 
Subject: Re: [gmx-users] Instantaneous Square Displacement
To: "Discussion list for GROMACS users" 
Date: Tuesday, March 8, 2011, 2:57 PM




Mark Abraham wrote:
> On 8/03/2011 3:01 AM, Jennifer Williams wrote:
>> 
>> Hi,
>> 
>> I am writing a paper where I describe that gas molecules move inside a pore 
>> and then stick for long periods of time in occlusions in the pore wall.
>> 
>> A reviewer has mentioned that I could illustrate this effect by using 
>> "instantaneous square-displacement".
>> 
>> I have already produced MSD vs time plots and used them to obtain the self 
>> diffusion coefficient. Can someone shed some light on how I can obtain the 
>> instantaneous square displacement in gromacs?
> 
> I have no idea what "ISD" means, and Google doesn't know either :) Perhaps 
> they want to see the diffusion of a single molecule?
> 

Searching for "instantaneous square displacement" turns up very little (3 
results), but the last seems to be what you need, as long as this person is 
correct:

http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1

Section 2.3.3.

-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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Re: [gmx-users] g_rms and g_cluster

[shahid nayeem]

Hi Justin
If I make an index group with backbone and CA C N O group of the
concerned residues and then do least square fitting then do this
fitting is equivalent to backbone fitting first and then translating
to coincide CA of the residue of interest. Is there any other
programme developed for gromacs trajectory analysis where I can do
backbone fitting first and then translate to coincide CA of residue of
interest before calculating RMSD.
Shahid Nayeem

On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>>
>> I want to calculate RMSD of one side chain residue from simulation
>> trajectory after full backbone alignment as well as translating to
>> coincide CA of the residue of interest. Is it possible to do with
>> g_rms both backbone alignment as well as translating to coincide CA.
>
> Least-squares fitting is performed on whatever group you choose (i.e.
> backbone), and the calculation group can then be whatever you want.  You can
> use trjconv to do translational fitting, but I don't know that you can force
> g_rms to always align this certain atom and still perform a backbone fit;
> these two may work against one another, even if the difference is small.
>
>> Another clarification is that in gromacs g_cluster how can I use
>> greedy algorithm for clustering.
>
> What is a "greedy" algorithm?  The available methods are described in the
> manual and/or g_cluster -h.
>
> -Justin
>
>> Shahid Nayeem
>
> --
> 
>
> 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] QMMM

[Txema Mercero]

I did follow the Gaussian/Gromacs QM/MM set up guide too and was not successful.

On Tue, Mar 8, 2011 at 1:28 PM, Jack Shultz  wrote:
> Good luck. I followed the instructions and was not successful.
>
> On Tue, Mar 8, 2011 at 12:48 AM, Haresh  wrote:
>>
>> Hello everyone,
>>
>> I want install gromacs with mopac7 for qmmm.
>>
>> Can you guide me for installation procedure
>>
>> Thank you.
>>
>>
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