[gmx-users] area per lipid

[Shima Arasteh]

Hi,

I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to 
reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned 
in articles ), I let the system to be simulated for 40 seconds. To do so, I 
checked the area  per lipid every 10 ns. The results of area per lipid in each 
step are as below:

1.
Top leaflet: 60.44  

Bottom leaflet: 59.43 


2.
Top leaflet: 61.135
Bottom leaflet: 60.11

3.
Top leaflet: 61.40  

Bottom leaflet: 60.38

4.
Top leaflet: 60.27  

Bottom leaflet: 59.27

I expected it to approaches the expected amount steadily, but why did I get 
such a result? How can I get to the appropriate area  per lipid? 

Would you please give me suggestions? Any suggestions would be appreciated.

Thanks in advance.


Sincerely,
Shima
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Re: [gmx-users] Re:Ka/Kd

[lloyd riggs]

Dear All,

So I went over the below Ka/Kd...Seems doesnt fit for anything, the DelG I 
found doesnt change for components, and just fit my data for the first 20 
analysis by chance I guess, except for Ent and Enth calculations from doing 
PCA, which break down nicely.  In case anyone reads this.

I have another couple questions regarding graphing.

-Regarding the output from g_gyrate, with the -nz option.  Is there a script 
somewhere to turn the x,y slices into a 3D plot or something (its around 40 
slices for say an 8 Ang. Z , times each time point.  You can do it by hand, but 
that turns into plugging the numbers into a matrix by hand for 200 point per 
time frameand most spread sheet things I have used (qti, Gnu, MS office) 
dont allow the manipulation of the data properly for such a plot, as its not 
simple cut and paste as with most plots.  In the end, one would most likely 
only need 2-3 snapshots over a run (200 points each) to show say a density of 
gyration for extreems, but you would have to look at most of them visually to 
find proper ones, especially from multiple runs)

-the same for ramachondran.  I basically want to just turn specific residues 
Vs. normal into histograms or a matrix with simple distribution (a 1 added to 
each 2D point for each occupancy to plot 3D ramachondrans).  This is not as bad 
as the gyrate, but still turns into 200 points per simulation, times 20 or so 
simulations.  I already know grace can take a column and turn it into a 
histogram, but not in 2D grids.  This I am sure is somewhere (a script or 
software), but have no clue whom/where to ask.

Sincerely,

Stephan Watkins

 Original-Nachricht 
> Datum: Tue, 06 Nov 2012 13:18:48 +0100
> Von: "lloyd riggs" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:Ka/Kd

> Thank you for the reply,
> 
> Figured.  Needless to say though, the software using the pulled gives
> about the same as by hand (although diffusion constants are also guessed but
> fit into what the computer calculates as compared on a scale of
> lysozyme,,, xxx, Fab fragments) but can not do the forward/backward 
> (values of
> -65000.045/-74967.031), while the one way and integral give reasonable values,
> and the caculated (via g_hbond or g_hbond->g_analyze) DelG fits well also...
> 
> grüess
> 
> Stephan
> 
>  Original-Nachricht 
> > Datum: Mon, 05 Nov 2012 18:14:36 -0500
> > Von: Justin Lemkul 
> > An: Discussion list for GROMACS users 
> > Betreff: Re: [gmx-users] Re:Ka/Kd
> 
> > 
> > 
> > On 11/5/12 9:59 AM, lloyd riggs wrote:
> > > Quick question,
> > >
> > > I went and calculated the Ka/Kd with the g_hbond --> -g_analyze and
> just
> > wondered, if all my simulations are pulled, does it in the end make any
> > sense, or is there ways to compensate for this.  I assume the h_bond
> life
> > would be meaningless, as under a normal situation, 2 proteins h-bond
> lifes
> > could stretch into the seconds (minus fluctuation around a very small
> bound
> > area)...
> > >
> > 
> > Extracting equilibrium properties from a non-equilibrium simulation is
> > dicey, 
> > indeed.  I've never attempted such a thing myself, but I would think
> > determining 
> > Kd from deltaG would be more reliable, at least inasmuch as the deltaG
> > estimate 
> > is reliable (i.e., from umbrella sampling and a proper assessment of
> > errors).
> > 
> > -Justin
> > 
> > -- 
> > 
> > 
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > 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: Running Gromacs in Clusters

[Marcelo Depolo]

I'm gonna check all this informations, Chaban.

I'm not expert in this field and I have to study much more to follow your
suggestions. Soon, I return with some news.
For now, thanks everyone for your suggestions.

-- 
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Biochemistry and Molecular Biology Department
University of Viçosa - Brazil
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Re: [gmx-users] Freeze group atoms changing position

[Alex Marshall]

Just as an update, I ran the simulation using position restraints with
force constants set to 1 for each atom in the restrained waters, and
none jumped out of the nanotube. Thanks for the help!

On Thu, Nov 1, 2012 at 5:01 PM, Justin Lemkul  wrote:

>
>
> On 11/1/12 4:56 PM, Alex Marshall wrote:
>
>> I've created a position restraint file for the specific waters that I need
>> to immobilize, but I'm having a hard time getting grompp to apply it
>> successfully. No matter where I put #include "posre.itp" in my topology
>> file grompp returns fatal errors about the atomic indices being out of
>> bounds. Is it actually possible to only apply position restraints to some
>> molecules within a species and leave the rest alone?
>>
>>
> Yes, but you can't simply #include "spc.itp" and then call the position
> restraint file, for example.  You need a [moleculetype] for the entire
> block of water, since position restraints can only be applied per
> [moleculetype].
>
> -Justin
>
>  On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 10/31/12 3:55 PM, Alex Marshall wrote:
>>>
>>>  Chris, is that for freeze groups or position restraints?


  I will assume Chris was referring to the restraint method - you need an
>>> index file for creating the position restraint .itp file using genrestr.
>>>   It will save you a ton of time over doing it manually.
>>>
>>> -Justin
>>>
>>>
>>>   On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale <
>>>
 chris.ne...@mail.utoronto.ca> wrote:

   No need to rename... just make an .ndx group.

>
> -- original message --
>
> As I understand it, position restraints for an atom are set in the
> topology
> file and applied to that atom in each of that species. In order to
> restrain
> some but not all of the water I'd have to copy the topology of my water
> model and add the restraints, then rename (and group together) the
> atoms
> I
> want to freeze so that they're identified with the appropriate topology
> file. Does this sound like it would work? Is there some other way that
> you
> might do it?
>
> Thanks
>
> On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall 
> wrote:
>
>   Justin: I'll try using position restraints instead of freezing the
> water
>
>> in the tube. Thanks for the tip.
>>
>> Bogdan: I don't think I'm using constraints other than freeze groups.
>> I
>> wasn't using energy group exclusions though. I tried running the
>>
>>  simulation
>
>  from the same initial configuration with newly-defined energy groups
>> CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second
>> for
>> the free atoms. The list of exclusions reads:
>> energygrp_excl   = CNT_GRA_WAL_IN CNT_GRA_WAL_IN
>>
>> Long story short, I'm roughly 15 ns into the simulation and the same
>> two
>> waters have jumped. I'll check the manual again though. Thanks.
>>
>> On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu >
>>  gmail.com>wrote:
>
>
>>   On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall 
>>
>>>
>>>  wrote:
>>
>
>  Thanks Justin. I identified the offending waters using vmd (adding 1
>>
>>>
  to
>>>
>>
>  resID and atom number since vmd starts counting at 0) and checked
>>
>>> confout.gro to make sure the coordinates matched up. I only have one

  group
>>>
>>>  for all frozen atoms in the system, and these guys are definitely in

  it.
>>>
>>
>
>>  Are you using some kind of constraints ? Are you using energy group
>>> exclusions to avoid interactions between frozen atoms ? If you search
>>> the manual for "frozen" you'll find some warnings and
>>> recommendations.
>>>
>>> Cheers,
>>> Bogdan
>>> --
>>> gmx-users mailing listgmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>>
>>> * Please search the archive at
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>>> posting!
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>>> >
>>>
>>>
>>>
>>
>> --
>> Alex Marshall
>> M.Sc. Candidate
>> Department of Applied Mathematics
>> The Uni

Re: [gmx-users] comparing gmx GB energy with Amber11

[Per Larsson]

Hi

A few things:

1. If I recall correctly, the GB-energy in gromacs is split into two parts, 
GB-polarization and non-polar solvation. Can you check whether this is the case 
and if the value you report is the sum of those two terms.

2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a 
slightly different part of the code to do the GB-calculation (you should see in 
your log file references to all-vs-all kernels)

3. Try running in single precision, keeping in mind 1 and 2 above to see if 
that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to 1 (at 
least it used to be called that, someone else can perhaps correct me if that 
has changed). This will make the code run without the sse-loops.

4. It could be that you are using different radii for the atoms in your system. 
For amber, are you using the Bondi-radii or something else?

Cheers
/Per


8 nov 2012 kl. 05:43 skrev Sandeep Somani:

> Hi,
> 
> I am comparing single point amber ff energies from gmx4.5.5 (double
> precision) and Amber11.
> 
> All bonded and non-bonded energy terms are in very good agreement (within
> 0.1 kJ/mol) except GB:
> gmx 'GB polarization' = -200 kJ/mol
> amber 11 'EGB' = -283 kJ/mol.
> 
> I am basically trying to replicate Amber's "igb=5 + large cutoff" in gmx.
> According to Amber manual igb=5 corresponds to "model 2 of [2004 OBC
> paper]".
> 
> I translated this to the following mdp options:
>  
> implicit_solvent= GBSA
> gb_algorithm= OBC
> All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of the
> molecule.
> {gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta, gb_obc_gamma,
> gb_dielectric_offset} = corresponding Amber input.
>  
> 
> Is that correct?
> 
> I realize that this is as much a question for Amber mailing list, but
> trying here first! Any idea?
> 
> The molecule is ala-12. I'll be happy to send input files.
> 
> Thanks in advance
> 
> Sandeep
> 
> --
> Postdoc
> Wales Group
> Cambridge
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[gmx-users] GROMACS with different gcc and FFT versions but one unique *tpr file

[Thomas Schlesier]

Dear all,
i have access to a cluster on which GROMACS is compiled with a different 
version of GCC and a different FFT libary (compared to the local machine).
Will this affect simulationns if i prepare the *.tpr on the local 
machine and run the simulation on the cluster and the local machine?


Sorry if this is a dumb question. I could imagine that the two 
simulations will be not numerical identical due to the different FFT 
libaries, but how strong this effect is and what else could happen i 
have no idea...


Greetings
Thomas
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Re: [gmx-users] GROMACS with different gcc and FFT versions but one unique *tpr file

[Carsten Kutzner]

Hi Thomas,

the .tpr files you prepare should be identical if you prepare them with the same
Gromacs version - regardless of the compiler. You can check that with gmxdump 
and
a diff if you like.

If you run these .tpr files using different machines or different compilers they
will not be numerically identical. Even if you run them twice on the same 
machine
but with dynamic load balancing on, they will not be numerically identical any
more. 

Carsten


On Nov 8, 2012, at 3:43 PM, Thomas Schlesier  wrote:

> Dear all,
> i have access to a cluster on which GROMACS is compiled with a different 
> version of GCC and a different FFT libary (compared to the local machine).
> Will this affect simulationns if i prepare the *.tpr on the local machine and 
> run the simulation on the cluster and the local machine?
> 
> Sorry if this is a dumb question. I could imagine that the two simulations 
> will be not numerical identical due to the different FFT libaries, but how 
> strong this effect is and what else could happen i have no idea...
> 
> Greetings
> Thomas
> -- 
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Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner

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Re: [gmx-users] comparing gmx GB energy with Amber11

[Sandeep Somani]

Hi Per

Pls see inline comments:


> 1. If I recall correctly, the GB-energy in gromacs is split into two
> parts, GB-polarization and non-polar solvation. Can you check whether this
> is the case and if the value you report is the sum of those two terms.
>

Yes, gromacs prints out "GB Polarization" and "Nonpolar Sol."
corresponding to "EGB" and "ESURF", respectively, from Amber.
Right now I am just comparing EGB part (non polar also do not match but
since it is a much smaller contribution, will worry about that later!).



>
> 2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a
> slightly different part of the code to do the GB-calculation (you should
> see in your log file references to all-vs-all kernels)
>

Just tried -- no change.
(btw, i didnt know 0 => no-cutoff. thnx!)


>
> 3. Try running in single precision, keeping in mind 1 and 2 above to see
> if that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to 1
> (at least it used to be called that, someone else can perhaps correct me if
> that has changed). This will make the code run without the sse-loops.
>
> I'll try shortly.


> 4. It could be that you are using different radii for the atoms in your
> system. For amber, are you using the Bondi-radii or something else?
>
> I tried both "set default PBradii mbondi" and "set default PBradii
mbondi2" while creating amber prmtop files in leap. The difference in EGB
is just 2-3 kcal/mol .. not enough to bridge the gap.

Best
Sandeep







> Cheers
> /Per
>
>
> 8 nov 2012 kl. 05:43 skrev Sandeep Somani:
>
> > Hi,
> >
> > I am comparing single point amber ff energies from gmx4.5.5 (double
> > precision) and Amber11.
> >
> > All bonded and non-bonded energy terms are in very good agreement (within
> > 0.1 kJ/mol) except GB:
> > gmx 'GB polarization' = -200 kJ/mol
> > amber 11 'EGB' = -283 kJ/mol.
> >
> > I am basically trying to replicate Amber's "igb=5 + large cutoff" in gmx.
> > According to Amber manual igb=5 corresponds to "model 2 of [2004 OBC
> > paper]".
> >
> > I translated this to the following mdp options:
> >  
> > implicit_solvent= GBSA
> > gb_algorithm= OBC
> > All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of
> the
> > molecule.
> > {gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta,
> gb_obc_gamma,
> > gb_dielectric_offset} = corresponding Amber input.
> >  
> >
> > Is that correct?
> >
> > I realize that this is as much a question for Amber mailing list, but
> > trying here first! Any idea?
> >
> > The molecule is ala-12. I'll be happy to send input files.
> >
> > Thanks in advance
> >
> > Sandeep
> >
> > --
> > Postdoc
> > Wales Group
> > Cambridge
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Hi
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Re: [gmx-users] constraining multiple types of bonds

[Justin Lemkul]

On 11/8/12 1:07 PM, tarak karmakar wrote:

Dear All,


In my system I need to fix three types of bonds

1) Metal-Ligand distance at a particular value given in PDB ( not covalent)


These require a merged [moleculetype] and are best implemented using simple 
harmonic interactions (bond type 6) or distance restraints.



2) I need to fix some of the bond lengths (covalent) for the substrate molecule.


Some, but not all?  That doesn't make sense to me.


3) Lastly the covalent H-bonds ( C-H, N-H, O-H etc.)



These are created using the .mdp settings shown below.

-Justin



My input .mdp file is given below

; 7.3.3 Run Control
integrator  = md-vv ; md integrator
tinit   = 0 ; [ps] starting time for run
dt  = 0.001 ; [ps] time step for integration
nsteps  = 500   ; maximum number of
steps to integrate, 0.001 * 20,00,000 = 2 ns
nstcomm = 1 ; [steps] frequency of
mass motion removal
comm_grps   = Protein Non-Protein   ; group(s) for center
of mass motion removal

; 7.3.8 Output Control
nstxout = 5000 ; [steps] freq to write
coordinates to trajectory
nstvout = 5000 ; [steps] freq to write
velocities to trajectory
nstfout = 5000 ; [steps] freq to write
forces to trajectory
nstlog  = 1000 ; [steps] freq to write
energies to log file
nstenergy   = 1000 ; [steps] freq to write
energies to energy file
nstxtcout   = 1000 ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision   = 1000 ; [real] precision to
write xtc trajectory
xtc_grps= System; group(s) to write to
xtc trajectory
energygrps  = System; group(s) to write to
energy file

; 7.3.9 Neighbor Searching
nstlist = 1 ; [steps] freq to
update neighbor list
ns_type = grid  ; method of updating
neighbor list
pbc = xyz   ; periodic boundary
conditions in all directions
rlist   = 1.2   ; [nm] cut-off
distance for the short-range neighbor list

nsttcouple  = 1
nstpcouple  = 1

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald
electrostatics
rcoulomb= 1.2   ; [nm] distance for
Coulomb cut-off

; 7.3.11 VdW
vdwtype = cut-off   ; twin-range cut-off
with rlist where rvdw >= rlist
rvdw= 1.2   ; [nm] distance for LJ cut-off
DispCorr= EnerPres  ; apply long range
dispersion corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.12  ; [nm] grid spacing
for FFT grid when using PME
pme_order   = 4 ; interpolation order
for PME, 4 = cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl  = Nose-Hoover   ; Nose-Hoover
temperature coupling
tc_grps = ProteinNon-Protein; groups to
couple seperately to temperature bath
tau_t   = 1.01.0; [ps] time
constant for coupling
ref_t   = 300300; [K]
reference temperature for coupling

; 7.3.15 Pressure Coupling
pcoupl  = MTTK  ; pressure
coupling where box vectors are variable
pcoupltype  = isotropic ; pressure
coupling in x-y-z directions
tau_p   = 1.0   ; [ps] time
constant for coupling
compressibility = 4.5e-5; [bar^-1]
compressibility
ref_p   = 1.0   ; [bar]
reference pressure for coupling

; 7.3.17 Velocity Generation
gen_vel = no; velocity
generation turned off

; 7.3.18 Bonds
constraints = h-bonds
constraint_algorithm= SHAKE ; SHAKE
Constraint Solver
shake_tol   = 1.0e-5




So I'm bit confused how to implement constraints algorithm for these
type of problem. If I do use the above set up then it is showing
following error

Program mdrun, VERSION 4.5.5
Source code file: invblock.c, line: 79

Fatal error:
Double entries in block structure. Item 5247 is in blocks 1371 and 1370
  Cannot make an unambiguous inverse block.


Thanks



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu 

Re: [gmx-users] area per lipid

[Justin Lemkul]

On 11/8/12 4:39 AM, Shima Arasteh wrote:

Hi,

I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to 
reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned 
in articles ), I let the system to be simulated for 40 seconds. To do so, I 
checked the area  per lipid every 10 ns. The results of area per lipid in each 
step are as below:

1.
Top leaflet: 60.44

Bottom leaflet: 59.43


2.
Top leaflet: 61.135
Bottom leaflet: 60.11

3.
Top leaflet: 61.40

Bottom leaflet: 60.38

4.
Top leaflet: 60.27

Bottom leaflet: 59.27

I expected it to approaches the expected amount steadily, but why did I get 
such a result? How can I get to the appropriate area  per lipid?

Would you please give me suggestions? Any suggestions would be appreciated.



Without seeing a complete .mdp file, it's hard to say.  Why are you picking 
snapshots every 10 ns?  You can easily plot APL over time for the entire 
trajectory using the box vectors stored in the .edr file from (Box-X * 
Box-Y)/(number of lipids).  You would have to write your own script to do the 
calculation, but it's quite straightforward.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] comparing gmx GB energy with Amber11

[Per Larsson]

Hi

Thanks for doing those test. They are all reassuring, I think.
Could you maybe send me your input-files off list and I'll take a look. 
I suspect the issue is that different radii are being used, as Gromacs does not 
use the Bondi radii.

Cheers
/Per


8 nov 2012 kl. 16:35 skrev Sandeep Somani:

> Hi Per
> 
> Pls see inline comments:
> 
> 
>> 1. If I recall correctly, the GB-energy in gromacs is split into two
>> parts, GB-polarization and non-polar solvation. Can you check whether this
>> is the case and if the value you report is the sum of those two terms.
>> 
> 
> Yes, gromacs prints out "GB Polarization" and "Nonpolar Sol."
> corresponding to "EGB" and "ESURF", respectively, from Amber.
> Right now I am just comparing EGB part (non polar also do not match but
> since it is a much smaller contribution, will worry about that later!).
> 
> 
> 
>> 
>> 2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a
>> slightly different part of the code to do the GB-calculation (you should
>> see in your log file references to all-vs-all kernels)
>> 
> 
> Just tried -- no change.
> (btw, i didnt know 0 => no-cutoff. thnx!)
> 
> 
>> 
>> 3. Try running in single precision, keeping in mind 1 and 2 above to see
>> if that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to 1
>> (at least it used to be called that, someone else can perhaps correct me if
>> that has changed). This will make the code run without the sse-loops.
>> 
>> I'll try shortly.
> 
> 
>> 4. It could be that you are using different radii for the atoms in your
>> system. For amber, are you using the Bondi-radii or something else?
>> 
>> I tried both "set default PBradii mbondi" and "set default PBradii
> mbondi2" while creating amber prmtop files in leap. The difference in EGB
> is just 2-3 kcal/mol .. not enough to bridge the gap.
> 
> Best
> Sandeep
> 
> 
> 
> 
> 
> 
> 
>> Cheers
>> /Per
>> 
>> 
>> 8 nov 2012 kl. 05:43 skrev Sandeep Somani:
>> 
>>> Hi,
>>> 
>>> I am comparing single point amber ff energies from gmx4.5.5 (double
>>> precision) and Amber11.
>>> 
>>> All bonded and non-bonded energy terms are in very good agreement (within
>>> 0.1 kJ/mol) except GB:
>>> gmx 'GB polarization' = -200 kJ/mol
>>> amber 11 'EGB' = -283 kJ/mol.
>>> 
>>> I am basically trying to replicate Amber's "igb=5 + large cutoff" in gmx.
>>> According to Amber manual igb=5 corresponds to "model 2 of [2004 OBC
>>> paper]".
>>> 
>>> I translated this to the following mdp options:
>>> 
>>> implicit_solvent= GBSA
>>> gb_algorithm= OBC
>>> All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of
>> the
>>> molecule.
>>> {gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta,
>> gb_obc_gamma,
>>> gb_dielectric_offset} = corresponding Amber input.
>>> 
>>> 
>>> Is that correct?
>>> 
>>> I realize that this is as much a question for Amber mailing list, but
>>> trying here first! Any idea?
>>> 
>>> The molecule is ala-12. I'll be happy to send input files.
>>> 
>>> Thanks in advance
>>> 
>>> Sandeep
>>> 
>>> --
>>> Postdoc
>>> Wales Group
>>> Cambridge
>>> --
>>> 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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Re: [gmx-users] comparing gmx GB energy with Amber11

[Sandeep Somani]

Hi Per

I tried with single precision gmx as well. No change.

Will send you input files soon.

Best
Sandeep

On Thu, Nov 8, 2012 at 3:55 PM, Per Larsson  wrote:

> Hi
>
> Thanks for doing those test. They are all reassuring, I think.
> Could you maybe send me your input-files off list and I'll take a look.
> I suspect the issue is that different radii are being used, as Gromacs
> does not use the Bondi radii.
>
> Cheers
> /Per
>
>
> 8 nov 2012 kl. 16:35 skrev Sandeep Somani:
>
> > Hi Per
> >
> > Pls see inline comments:
> >
> >
> >> 1. If I recall correctly, the GB-energy in gromacs is split into two
> >> parts, GB-polarization and non-polar solvation. Can you check whether
> this
> >> is the case and if the value you report is the sum of those two terms.
> >>
> >
> > Yes, gromacs prints out "GB Polarization" and "Nonpolar Sol."
> > corresponding to "EGB" and "ESURF", respectively, from Amber.
> > Right now I am just comparing EGB part (non polar also do not match but
> > since it is a much smaller contribution, will worry about that later!).
> >
> >
> >
> >>
> >> 2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a
> >> slightly different part of the code to do the GB-calculation (you should
> >> see in your log file references to all-vs-all kernels)
> >>
> >
> > Just tried -- no change.
> > (btw, i didnt know 0 => no-cutoff. thnx!)
> >
> >
> >>
> >> 3. Try running in single precision, keeping in mind 1 and 2 above to see
> >> if that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to
> 1
> >> (at least it used to be called that, someone else can perhaps correct
> me if
> >> that has changed). This will make the code run without the sse-loops.
> >>
> >> I'll try shortly.
> >
> >
> >> 4. It could be that you are using different radii for the atoms in your
> >> system. For amber, are you using the Bondi-radii or something else?
> >>
> >> I tried both "set default PBradii mbondi" and "set default PBradii
> > mbondi2" while creating amber prmtop files in leap. The difference in EGB
> > is just 2-3 kcal/mol .. not enough to bridge the gap.
> >
> > Best
> > Sandeep
> >
> >
> >
> >
> >
> >
> >
> >> Cheers
> >> /Per
> >>
> >>
> >> 8 nov 2012 kl. 05:43 skrev Sandeep Somani:
> >>
> >>> Hi,
> >>>
> >>> I am comparing single point amber ff energies from gmx4.5.5 (double
> >>> precision) and Amber11.
> >>>
> >>> All bonded and non-bonded energy terms are in very good agreement
> (within
> >>> 0.1 kJ/mol) except GB:
> >>> gmx 'GB polarization' = -200 kJ/mol
> >>> amber 11 'EGB' = -283 kJ/mol.
> >>>
> >>> I am basically trying to replicate Amber's "igb=5 + large cutoff" in
> gmx.
> >>> According to Amber manual igb=5 corresponds to "model 2 of [2004 OBC
> >>> paper]".
> >>>
> >>> I translated this to the following mdp options:
> >>> 
> >>> implicit_solvent= GBSA
> >>> gb_algorithm= OBC
> >>> All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of
> >> the
> >>> molecule.
> >>> {gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta,
> >> gb_obc_gamma,
> >>> gb_dielectric_offset} = corresponding Amber input.
> >>> 
> >>>
> >>> Is that correct?
> >>>
> >>> I realize that this is as much a question for Amber mailing list, but
> >>> trying here first! Any idea?
> >>>
> >>> The molecule is ala-12. I'll be happy to send input files.
> >>>
> >>> Thanks in advance
> >>>
> >>> Sandeep
> >>>
> >>> --
> >>> Postdoc
> >>> Wales Group
> >>> Cambridge
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> * Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-requ...@gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> 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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> >> www interface or send it to gmx-users-requ...@gromacs.org.
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> >>
> > Hi
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Running Gromacs in Clusters

[Szilárd Páll]

Hi,

With a fast network like Cray's you can easily get to 400-500 atoms/core
core with 4.5 (that's 400+ cores for your system), perhaps even further.
With 4.6 this improves quite a bit (up to 2-3x).

--
Szilárd


On Wed, Nov 7, 2012 at 5:19 PM, Erik Marklund  wrote:

> Hi,
>
> Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms
> on 192 cores at ~45 ns a day. with half the number of processors I get ~27
> ns a day. It will of course depend on the hardware, particular algorithms,
> run parameters, and on the system details.
>
> Erik
>
> 7 nov 2012 kl. 16.51 skrev Marcelo Depolo:
>
> > Good afternoon,
> >
> >
> > I wonder if anyone has experience running Gromacs in MPI. I'm
> paralleling the
> > processes and want to know how many processors reduces the computation
> time to
> > the minimum. I am currently using 24 processors for a system of 170 000
> > atoms and obtaining a simulation of 50ns in 15 days. There's a way to
> > reduce more this computational time?
> >
> > Thanks in advance!
> > --
> > Marcelo Depólo Polêto
> > Departamento de Bioquímica e Biologia Molecular
> > Universidade Federal de Viçosa - UFV
> > *Website: http://opensourcebioinformatics.com/site/*
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
> --
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Re: [gmx-users] constraining multiple types of bonds

[tarak karmakar]

Thanks Justin
As you see in the .mdp file I have used SHAKE. So if I want to fix
some C-C or C-O then what algorithm I have to use ?

In my topology file I have specified following bonds to be
constrained. The first two are covalent and the last one is M-L
non-covalent bond.

[ constraints ]
;  index1  index2   funct  length(nm)
6062   6063   10.1149000
6062   6064   10.1149000
6060   4309   10.210
Now while implementing SHAKE it is showing

Program mdrun, VERSION 4.5.5
Source code file: invblock.c, line: 79

Fatal error:
Double entries in block structure. Item 5247 is in blocks 1371 and 1370
  Cannot make an unambiguous inverse block.

Please suggest me the exact protocol.
Thanks

On Fri, Nov 9, 2012 at 2:18 AM, Justin Lemkul  wrote:
>
>
> On 11/8/12 1:07 PM, tarak karmakar wrote:
>>
>> Dear All,
>>
>>
>> In my system I need to fix three types of bonds
>>
>> 1) Metal-Ligand distance at a particular value given in PDB ( not
>> covalent)
>
>
> These require a merged [moleculetype] and are best implemented using simple
> harmonic interactions (bond type 6) or distance restraints.
>
>
>> 2) I need to fix some of the bond lengths (covalent) for the substrate
>> molecule.
>
>
> Some, but not all?  That doesn't make sense to me.
>
>
>> 3) Lastly the covalent H-bonds ( C-H, N-H, O-H etc.)
>>
>
> These are created using the .mdp settings shown below.
>
> -Justin
>
>
>>
>> My input .mdp file is given below
>>
>> ; 7.3.3 Run Control
>> integrator  = md-vv ; md integrator
>> tinit   = 0 ; [ps] starting time
>> for run
>> dt  = 0.001 ; [ps] time step for
>> integration
>> nsteps  = 500   ; maximum number of
>> steps to integrate, 0.001 * 20,00,000 = 2 ns
>> nstcomm = 1 ; [steps] frequency of
>> mass motion removal
>> comm_grps   = Protein Non-Protein   ; group(s) for center
>> of mass motion removal
>>
>> ; 7.3.8 Output Control
>> nstxout = 5000 ; [steps] freq to write
>> coordinates to trajectory
>> nstvout = 5000 ; [steps] freq to write
>> velocities to trajectory
>> nstfout = 5000 ; [steps] freq to write
>> forces to trajectory
>> nstlog  = 1000 ; [steps] freq to write
>> energies to log file
>> nstenergy   = 1000 ; [steps] freq to write
>> energies to energy file
>> nstxtcout   = 1000 ; [steps] freq to write
>> coordinates to xtc trajectory
>> xtc_precision   = 1000 ; [real] precision to
>> write xtc trajectory
>> xtc_grps= System; group(s) to write to
>> xtc trajectory
>> energygrps  = System; group(s) to write to
>> energy file
>>
>> ; 7.3.9 Neighbor Searching
>> nstlist = 1 ; [steps] freq to
>> update neighbor list
>> ns_type = grid  ; method of updating
>> neighbor list
>> pbc = xyz   ; periodic boundary
>> conditions in all directions
>> rlist   = 1.2   ; [nm] cut-off
>> distance for the short-range neighbor list
>>
>> nsttcouple  = 1
>> nstpcouple  = 1
>>
>> ; 7.3.10 Electrostatics
>> coulombtype = PME   ; Particle-Mesh Ewald
>> electrostatics
>> rcoulomb= 1.2   ; [nm] distance for
>> Coulomb cut-off
>>
>> ; 7.3.11 VdW
>> vdwtype = cut-off   ; twin-range cut-off
>> with rlist where rvdw >= rlist
>> rvdw= 1.2   ; [nm] distance for LJ
>> cut-off
>> DispCorr= EnerPres  ; apply long range
>> dispersion corrections for energy
>>
>> ; 7.3.13 Ewald
>> fourierspacing  = 0.12  ; [nm] grid spacing
>> for FFT grid when using PME
>> pme_order   = 4 ; interpolation order
>> for PME, 4 = cubic
>> ewald_rtol  = 1e-5  ; relative strength of
>> Ewald-shifted potential at rcoulomb
>>
>> ; 7.3.14 Temperature Coupling
>> tcoupl  = Nose-Hoover   ; Nose-Hoover
>> temperature coupling
>> tc_grps = ProteinNon-Protein; groups to
>> couple seperately to temperature bath
>> tau_t   = 1.01.0; [ps] time
>> constant for coupling
>> ref_t   = 300300; [K]
>> reference temperature for coupling
>>
>> ; 7.3.15 Pressure Coupling
>> pcoupl  = MTTK  ; pressure
>> coupling where box vectors are variable
>> pcoupltype  = isotropic ; pres

Re: [gmx-users] area per lipid

[Shima Arasteh]

I pick the snapshots every 10ns, because I don't know how much time this system 
needs to be simulated to reach to the proper APL.

The md.mdp dile I used here is:

title        = Production run for Water-POPC system

; Parameters describing the details of the NVT simulation protocol
integrator    = md        
dt        = 0.002            
nsteps        = 500    

; Parameters controlling output writing
nstxout        = 1000        
nstvout        = 1000        
nstenergy    = 1000        
nstlog        = 1000        

; Parameters describing neighbors searching and details about interaction 
calculations
ns_type        = grid    
nstlist        = 5        
rlist        = 1.2    
rcoulomb    = 1.2    
rvdw        = 1.2    
pbc        = xyz        

; Parameters for treating bonded interactions
continuation    = yes            
constraint_algorithm = LINCS    
constraints    = all-bonds            
lincs_iter    = 1                    
lincs_order    = 4                    

; Parameters for treating electrostatic interactions
coulombtype    = PME            
pme_order    = 4                
fourierspacing    = 0.16        

; Temperature coupling parameters
tcoupl        = Nose-Hoover    
tc-grps        = POPC SOL         
tau_t        = 0.5    0.5     
ref_t        = 300     300        

; Pressure coupling parameters
pcoupl        = Parrinello-Rahman        
pcoupltype    = semiisotropic            
tau_p        = 2.0                   
ref_p        = 1.0    1.0                  
compressibility = 4.5e-5    4.5e-5    


DispCorr    = EnerPres        
gen_vel        = no             
nstcomm        = 1            
comm_mode    = Linear    
comm_grps    =POPC SOL    



Sincerely,
Shima



From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Friday, November 9, 2012 12:20 AM
Subject: Re: [gmx-users] area per lipid



On 11/8/12 4:39 AM, Shima Arasteh wrote:
> Hi,
>
> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order 
> to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as 
> mentioned in articles ), I let the system to be simulated for 40 seconds. To 
> do so, I checked the area  per lipid every 10 ns. The results of area per 
> lipid in each step are as below:
>
> 1.
> Top leaflet: 60.44
>
> Bottom leaflet: 59.43
>
>
> 2.
> Top leaflet: 61.135
> Bottom leaflet: 60.11
>
> 3.
> Top leaflet: 61.40
>
> Bottom leaflet: 60.38
>
> 4.
> Top leaflet: 60.27
>
> Bottom leaflet: 59.27
>
> I expected it to approaches the expected amount steadily, but why did I get 
> such a result? How can I get to the appropriate area  per lipid?
>
> Would you please give me suggestions? Any suggestions would be appreciated.
>

Without seeing a complete .mdp file, it's hard to say.  Why are you picking 
snapshots every 10 ns?  You can easily plot APL over time for the entire 
trajectory using the box vectors stored in the .edr file from (Box-X * 
Box-Y)/(number of lipids).  You would have to write your own script to do the 
calculation, but it's quite straightforward.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
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] Protein at given pH

[Tsjerk Wassenaar]

Hi,

Do you mean the pKa value of the side chain in solution? Or the pKa value
in ethanol, DMSO, hexane? Maybe the pKa value in a membrane, or in the
interior of a protein, perhaps in a hydrophobic pocket? Or the pKa with
one/two/three neighbouring acidic/basic residues? If you have literature
values applying to your case, sure, go ahead and use them!

Cheers,

Tsjerk


On Wed, Nov 7, 2012 at 4:21 PM, Steven Neumann wrote:

> On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund 
> wrote:
> > Hi,
> >
> > I've used the H++ server myself at times. My experience is that it's
> rather sensitive to the very fine detail of the input structure in some
> cases. I've had situations where H++ suggest one protonation state, then a
> short md simulation takes the system to a slightly different conformation
> that seem more prevalent but that yields another protonation state if sent
> to H++ again. Use all biochemical knowledge that you can muster to check
> that the output makes sense. Focus on residues that you suspect might be
> important for the overall question you address.
> >
> > That said, pKa calculations are inherently difficult and can probably
> not be done reliably without lots of simulations. As such H++ probably come
> close to what we can currently accomplish within reasonable time for
> (nearly) static structures.
> >
> > Best,
> >
> > Erik
>
> Thanks for this! Is it not better just to use pK values from the
> literature corresponding to given residue side chain? My protein is an
> alpha-helix.
>
> Thanks,
>
> Steven
>
>
> >
> > 7 nov 2012 kl. 10.19 skrev Steven Neumann:
> >
> >> Dear Gmx Users,
> >>
> >> I am trying to simulate protein-ligand interactions at specific pH=5.
> >> I processed my protein.pdb into the H++. As I see from th titration
> >> curve of the entire molecule it appears that at pH=5 the total charge
> >> should be equal to 2. When I process the obtained pdb from the server
> >> to pdb2gmx using -ignh I get the total charge of -3. Can anyone
> >> explain me this?
> >>
> >> In terms of small molecules how can I get parameters at specific pH? I
> >> am using Charmm and parachem.org does not support pH changes. Can
> >> anyone advise?
> >>
> >> thank you,
> >>
> >> Steven
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
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> >
> > ---
> > Erik Marklund, PhD
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,75124 Uppsala, Sweden
> > phone:+46 18 471 6688fax: +46 18 511 755
> > er...@xray.bmc.uu.se
> > http://www2.icm.uu.se/molbio/elflab/index.html
> >
> > --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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