from:"lloyd riggs"

Aw: [gmx-users] DPOSRES and energy minimization

2013-11-03 Thread lloyd riggs


all-bonds and none work, so I assume, as alternating between these settings speeds up the EM.  However, I always see the protein move around in the box after centering, so just re-center after reaching pressure and temp stability before the extended pre-run equilibration with set restraints (which seems to keep the protein where I want at this point).

 

Sincerely,

 

Stephan Watkins

 

Gesendet: Sonntag, 03. November 2013 um 05:38 Uhr
Von: "Gianluca Interlandi" 
An: "Discussion list for GROMACS users" 
Betreff: [gmx-users] DPOSRES and energy minimization

Is it possible to use position restraints: define = -DPOSRES during an energy minimization? I tried to do that but it looks like all atoms are moved during minimization: ; VARIOUS PREPROCESSING OPTIONS = title = cpp = /lib/cpp include = define = -DPOSRES ; IMPLICIT SOLVENT OPTIONS = implicit-solvent = GBSA gb-algorithm = OBC ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.001 nsteps = 1000 ; ENERGY MINIMIZATION OPTIONS = emtol = 0.1 emstep = 0.01 nstcgsteep = 1000 Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing list gmx-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



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Aw: Re: [gmx-users] Constant-Force Pulling of Ubiquitin

2013-10-29 Thread lloyd riggs


I dont know how well v-rescale works with pulling.  It could be after removing some restraints it still had not reached a good equilibrium (ie let it run a while/nanosecound or 5, before pulling it), or maybe generating velocities on start causes more caos than the proteins or system can handle, still it may be the real system minus several initial time frames, ie it either isnt bound from the start as it is in reality or it prefers to be free...But I may be wrong on some of this...so just suggestions.  Also, 500 picoseconds is short for measring things, and would probably be dominated by starting velocity for at least 40-80 picoseconds, thus look at how fast it declines...there are some printed standards for protein-protein delG or domain changes of around 3-4 ns to make sure small loop/domain changes are represented in the energy profile.  There was (on some comments) talk of making this around 6 ns..but I dont know if there are set real standards for this held fast to (i've read 2 papers with 400 ns to see domain changes with no pull, and a good 5-6 at 4 ns with pulling so?).

 

Stephan Wakins

 

Gesendet: Dienstag, 29. Oktober 2013 um 20:27 Uhr
Von: "XAvier Periole" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] Constant-Force Pulling of Ubiquitin


You want to switch to sd instead of md.

> On Oct 29, 2013, at 17:43, Vivian  wrote:
>
> Hi GMX Users,
>
> I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin
> and it's a implicit model. My mdp file for pulling is shown as following.
>
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 50 ; total 500 ps.
>
> nstxout = 100
> nstvout = 100
> nstfout = 100
> nstlist = 10
> nstlog = 100
> nstcalcenergy =100
>
> rlist = 5
> rvdw = 5
> rcoulomb = 5
> coulombtype = cut-off
> vdwtype = cut-off
> table-extension = 5
> bd_fric = 0
> ld_seed = -1
> pbc = no
> ns_type = simple
> constraints = all-bonds
> lincs_order = 4
> lincs_iter = 1
> lincs-warnangle = 30
>
> Tcoupl = v-rescale
> tau_t = 1.0
> tc-grps = Protein
> ref_t = 300
>
> Pcoupl = no
>
> gen_vel = yes
> gen_temp = 300
> gen_seed = 173529
>
> comm_mode = Angular
> nstcomm =100
>
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent = gbsa
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 5
> ; Dielectric coefficient of the implicit solvent
> gb_epsilon_solvent = 80
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> gb_dielectric_offset = 0.009
> sa_algorithm = Ace-approximation
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
> ; The value -1 will set default value for Still/HCT/OBC GB-models.
> sa_surface_tension = 2.05016
>
> ; Pull code
> pull = constant_force
> ;Center of mass pulling using a linear potential and therefore a constant
> force.
> pull_geometry = direction
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group1 = Chain_B
> pull_group0 = Chain_A
> pull_k1 = -500 ; kJ mol^-1 nm^-2
> pull_vec1 = 0.0 0.0 1.0
>
> However, after pulling simulation, it turns out the potential of this system
> becomes lower rather than higher (from -1 to -2). It's very wired
> since potential should become larger after pulling.
> Here is the notification after g_energy:
>
> Energy Average Err.Est. RMSD Tot-Drift
> ---
> Potential -20734.5 230 1268.47 -1385.71
> (kJ/mol)
>
> You may want to use the -driftcorr flag in order to correct for spurious
> drift in the graphs. Note that this is not
> a substitute for proper equilibration and sampling! You should select the
> temperature in order to obtain fluctuation properties.
>
> I wonder whether there is any problem with my mdp file.
> Thank you so much!!
>
> Best,
> Vivian
>
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[gmx-users] RE:Requests

2013-10-27 Thread lloyd riggs


 

>You are not allowed to post to this mailing list, and your message has
>been automatically rejected. If you think that your messages are
>being rejected in error, contact the mailing list owner at
>gmx-developers...

 

Sorry I was trying to post this to the "Feature suggestion/request" site on gromacs mailserver, however this has been changed in recent months.  I thus do not know how to post such a thing now without joining the developer mail site (I would at present not be such a person, and would not like to see such a thing bogged down with user help mails/spam).

 

I was just attempting to run this by some developers.  In the past two years I have run into several materials based work which would benifit from electric currents, or electomagnetic fields (external broad range in setting).  In the recent science there was a nice piece about this applied to liquid droplets with particles, or doped secoundary chemistry (oils, polymers, complex small molecule/metal adducts and/or nano bead polymers...), which primarily work through external magnetic field altering the surface chemistry, and retaining the effects after fields are removed.  This can also be applied to electromagentic induced crystalization at atomic level, multi layered liquid interfaces...etc.

 

In any case this might be an area where simulations would play a large part if effects from external fields, or even free electrons (currents applied in layers, surfaces or the entire unit cell) could be modeled sufficiently.  Meaning probably a good lab funding source and interesting work.

 

Sorry about any spelling areas.

 

Sincerely,

 

Stephan Watkins, (now PhDd)

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Aw: RE: [gmx-users] Continuing runs from 4.5.4 in 4.6.3

2013-10-23 Thread lloyd riggs


I ran into this, you basically should determine your time frame, and install 4.5.4 if its a problem local (only 1-2 hours), to finish the work, otherwise you need to start from scratch.  But I did this with older versions, so do not know about higher versions (such as if the programmers eliminated the read version number thing at many of the script initializing things...).  The auxillary software does work for analysis, but you end up having to cut things into portions with some aspects, 1/2 one version versus 1/2 the other...but mostly for higher end analysis, not the simplistic ones, such as distance versus hessian matrices or covariance.

 

Stephan Watkins

 

Gesendet: Mittwoch, 23. Oktober 2013 um 16:17 Uhr
Von: "Kevin Chen" 
An: "'Discussion list for GROMACS users'" 
Betreff: RE: [gmx-users] Continuing runs from 4.5.4 in 4.6.3

There shouldn't be a problem for that. BTW, can you also enter a ticket at
Daigrid.org for this matter?

Thanks

-Kevin


-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of rajat desikan
Sent: Wednesday, October 23, 2013 1:24 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Continuing runs from 4.5.4 in 4.6.3

Hi,

We recently had a software upgrade in our cluster from gromacs 4.5.4. to
gromacs 4.6.3.. I need to continue an earlier simulation that had been run
in 4.5.4. using the .cpt, .tpr and .mdp.

Are there any issues with continuing these runs in 4.6.3.? Can I concatenate
these trajectories for later analysis?

I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4.

Any input will be appreciated. Thanks.

--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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This is my own experience, someone may have better suggestions. First, you can look on the internet for .py .c++ or java matix manupulation tools/small programs run in bash shells. These allow the output from the g:sham or other (2d or 3d) to be turned into mtricies. These can then be fed into qtiplot/scidavis matricies. You can also sum/n all of these for guassians to get your overall realistic maps. qtiplot makes nice images of matricies with thermal maps...also, with the 1980 .xpm files, you can just cut these (the mtrix portion) and feed them into qtiplot, and do all fo the same. There's a setting for real values (0.335587) vs 0 and 1, but I forget these, and then do the same for your guassian, and plot these in the same software. Mostly all of this is based on simple matix manipulation .py or .C++ found for free on the internetbut are doable for any projectothers might have better suggestions...

Stephan Watkins

Gesendet: Montag, 14. Oktober 2013 um 13:54 Uhr
Von: "pratibha kapoor"
An: gmx-users@gromacs.org
Betreff: [gmx-users] g_sham

Dear all gromacs users

I am creating free energy landscape using g_sham but my axis are not
getting labelled. I have searched the archive and found that using xmin and
xmax options we can label them.
I have first created my 2D projection xvg file using
g_anaeig -f *.xtc -s *.tpr -first 1 -last 2 -2d *.xvg -v *.trr
and then found min and max values for both the vectors,
say for vector1 min:-2.25 and max:1.83
and for vector2 min:-1.60 and max: 2.22
and then I have used:
g_sham -f *.xvg -ls *.xpm -notime -xmin -2.25 -1.60 0 -xmax 1.83 2.22 0
and then converted *.xpm to *.eps using
xpm2ps -f *.xpm -o *.eps -rainbow blue
This way I got eps file with only one axis(x axis) labelled and following
line appeared:
Auto tick spacing failed for Y-axis, guessing 1.19375

I would like to ask is this way of labelling the axis correct? If yes, why
didn't y axis get labelled and how to solve the problem?

Thanks in advance.
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Aw: [gmx-users] Force Field for peptides and proteins

2013-08-13 Thread lloyd riggs

There isn't one it depends on your experiment, and what factors you take into account such as resources, time available or what you wish to observe. All atom is more realistic, but if time retraints or computer resources are limiting, you may wish a partial atom or hybrid atom system. In addition, difference in simply looking at domain changes in proteins or affinites, etc...

Gesendet: Montag, 12. August 2013 um 14:19 Uhr
Von: "Maria Astón Serrano"
An: gmx-users@gromacs.org
Betreff: [gmx-users] Force Field for peptides and proteins

Dear Gromacs users,

We would like to know which is the Force Field which is customarily
preferred for simulations of peptides and proteins.

Thank you very much.

Best regards,

Maria
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Aw: [gmx-users] Umbrella sampling - position restraints

2013-08-08 Thread lloyd riggs

it more accuratly represents reality (my opinion), but is not feasable with high energy affinities such as protein-protein or DNA-protein interactions with short (under u or m seconds) and is used as such (I assume) in many things, or you cant pull them apart. A comparison however, would probably not show much difference ( a basketball with a small marble or even beebee thrown at it depending on what your looking at). I would say any published things should just maintain consistence, but trying one or two differences to see is research.

Stephan Watkins

Gesendet: Donnerstag, 08. August 2013 um 21:57 Uhr
Von: rookie417
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling - position restraints

Dear GROMACS users,

I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later
during analysis. The simulations ran normally and the PMF plots look
accurate. However, I realized that position restraints were not applied only
after looking at the log files and position restraints energy values were
missing. The umbrella sampling MD simulation was for 2 ns only and I checked
the pullx-umbrella.xvg files and the COM fluctuations are not that bad
considering its only a short time for convergence.

Can anyone comment on how not using position restraints would effect the
result otherwise?

Thanks

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Aw: Re: [gmx-users] Umbrella Sampling

2013-07-31 Thread lloyd riggs

I did this with a small molecule and the ions were in the solvent, but associated with the ligand, and conversly if the site has a Mg or something etc...it wouldn't be restrained in the normal posres.itp unless you made one for them.  It is in the end a matter of view, but I am assuming the change in the binding sites energy would reflect also the ions or the ions being attached to the ligand would not represent a completly solvated ligand (ie energy missing).  The positional restraint I stated meant you can just make a two ion -posres_ion and include it in an .mdp however it might screw your system up if your protein is not positionally restrained, or calphas etc...thus I dont know based on your experiment.  If the ions move into solution it probably doesnt matter (a quick visual of the simulation).  But somone else might have better ideas to help out.

Stephan

Gesendet: Mittwoch, 31. Juli 2013 um 12:46 Uhr
Von: "Steven Neumann" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] Umbrella Sampling

They do not dissociate...Are you sure? My mdp specifies only ligand as a
pull_group1. I think it would change having ions in this group included.

On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs  wrote:

>
> >will get the PMF profile for my
> >ligand binding or ligand and two ions binding?
>
> It would be the ligand and two ions unless the ions also at some point
> discossiate from the ligand once in solvent. Could add positional restraint
> for them, but dont know how that effects the calculation?
> *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
> *Von:* "Steven Neumann" 
> *An:* "Discussion list for GROMACS users" 
> *Betreff:* [gmx-users] Umbrella Sampling
> Dear Gmx Users,
>
> I run SMD to extract the windows for US calculations. The system involves
> negatively charged ligand and protein. I generated the protein-ligand
> complex within self assembly MD simulations.
>
> I pulled my molecule away and two ions were also detached from the protein
> surface being attached to my ligand.
>
> My question: if I run my US caluclation and combine windows by WHAM (I
> specified in my umbrella.mdp my ligand as a pull_group1 and same protein
> residues I pulled it from as pull_group0) will get the PMF profile for my
> ligand binding or ligand and two ions binding?
>
> Steven
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Aw: [gmx-users] Umbrella Sampling

2013-07-31 Thread lloyd riggs

>will get the PMF profile for my
>ligand binding or ligand and two ions binding?

It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation?

Gesendet: Mittwoch, 31. Juli 2013 um 09:29 Uhr
Von: "Steven Neumann"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] Umbrella Sampling

Dear Gmx Users,

I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.

I pulled my molecule away and two ions were also detached from the protein
surface being attached to my ligand.

My question: if I run my US caluclation and combine windows by WHAM (I
specified in my umbrella.mdp my ligand as a pull_group1 and same protein
residues I pulled it from as pull_group0) will get the PMF profile for my
ligand binding or ligand and two ions binding?

Steven
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Aw: [gmx-users] constant force pulling

2013-07-30 Thread lloyd riggs

 

Just read your other responses, didnt know it would overide with vector set, but if it doesnt work try the _dim

 

Stephan


Gesendet: Montag, 29. Juli 2013 um 20:42 Uhr
Von: kim2811 
An: gmx-users@gromacs.org
Betreff: [gmx-users] constant force pulling

Hi,

I am trying to pull/separate a protein dimer by applying constant force in
my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in
the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set
my simulation to run for 5 ns. However, after only 251 ps, I got this fatal
error:

Distance of pull group 1 (3.958423 nm) is larger than 0.49 times the box
size (16.314939)

Can somebody please interpret this error? When I checked the trajectory, the
protein seems to be inside the box or at least the COM of the dimer is near
the center of the box, so the protein approaching near the boundary can't be
the reason for this error. If it can help to clarify, here's my pull code:

; Pull code
pull = constant_force
pull_geometry = direction ; pull in the direction of pull code
pull_dim = Y Y Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = chain_A ; C-terminal of Protein 1
pull_group1 = chain_B ; C-terminal of Protein 2
pull_k1 = -500 ; kJ mol^-1 nm^-1
pull_vec1 = 0 1 0

Thank you.



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Aw: [gmx-users] constant force pulling

2013-07-30 Thread lloyd riggs

 

Your pulling it in all 3 directions at one time.  Also, you should check the COM you want to be pulling from, but I do not know your experimental design.  I would say look at Justins tutorial and example .mdp files.

 

Stephan Watkins


Gesendet: Montag, 29. Juli 2013 um 20:42 Uhr
Von: kim2811 
An: gmx-users@gromacs.org
Betreff: [gmx-users] constant force pulling

Hi,

I am trying to pull/separate a protein dimer by applying constant force in
my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in
the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set
my simulation to run for 5 ns. However, after only 251 ps, I got this fatal
error:

Distance of pull group 1 (3.958423 nm) is larger than 0.49 times the box
size (16.314939)

Can somebody please interpret this error? When I checked the trajectory, the
protein seems to be inside the box or at least the COM of the dimer is near
the center of the box, so the protein approaching near the boundary can't be
the reason for this error. If it can help to clarify, here's my pull code:

; Pull code
pull = constant_force
pull_geometry = direction ; pull in the direction of pull code
pull_dim = Y Y Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = chain_A ; C-terminal of Protein 1
pull_group1 = chain_B ; C-terminal of Protein 2
pull_k1 = -500 ; kJ mol^-1 nm^-1
pull_vec1 = 0 1 0

Thank you.



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Aw: [gmx-users] Free Energy Simulations in Parallel

2013-07-27 Thread lloyd riggs

Play with the domain decomposition, lincs itr/order, -ntomp and -ntmpi, etc... I was able to get a 4 day simulation which often gave that error to speed up to 12 hours on 24 CPU/3 nodes/144 cores but it took 2 days of submitting, checking speed, and killing jobs to try another grid routine. My problem related to this is it wont go any faster (more nodes, cpu's or cores and starts to hit limits where there are only 100 atoms in a unit cell) if anyone knows a way to make it go faster.

Sincerely,

Stephan Watkins

Gesendet: Freitag, 26. Juli 2013 um 22:13 Uhr
Von: "Quintin Sheridan"
An: "gmx-users@gromacs.org"
Betreff: [gmx-users] Free Energy Simulations in Parallel

Dear Gromacs Users,

Is it possible to run free energy calculations in parallel using mpirun?
If not, what is the fastest way to run free energy calculations. I am
trying to us the Bennet's Accepetance Ratio (g_bar) to get the free energy
of solvation for an ionic liquid based on the tutorial by Justin Lemkul. I
hav tried to decouple an ion pair as well as individual ions. In either
case the simulations run locally but when I try to run them in parrallel I
get the error:

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 2.26125 nm

Thank You
Quintin Sheridan
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Aw: [gmx-users] unable to equilibrate pressure in npt

2013-07-25 Thread lloyd riggs

Dear Amin,

I did such things in the past, and had similar issues. First of, somone may have beter suggestions. The coupling time will bring it down a bit in the .mdp file (0.2 Vs 2 picoseconds. However, I have found that you will still see large fluctuations around a mean once equilibrated which can vary by 10 to 60, 70 Atomospheres depending on the pressure coupling algorythim used. If it oscillates around this mean, without large up or down changes I assume it is eq'd. Basically, if you look at it from the perspective of what pressure itself entails, it is the direct kenetic force of small molecules bumping into each other, so a simple protein movmeent in a small unit cell is turned by the computer into a molar ration, which looks crazy at the macroscopic level, but in reality you do not usually have the unit cell in such a deminsion. This is of course unless your system is made of nothing other than small molecules, which take off a 0 to the oscillation range. the pressure algorythms just keep it from going to insanly large limits, such as an ice cube because of 200 kcal/mol - enthalpy or boiling in the reverse, by pretending there is a universal pressure applied to the unit cell...so a generalized correction for the fact that the unit cell is not really representing infinaty as it is treated by the computer...based on real macroscopic pressures. I may be wrong , but this is my assumption.

Stephan Watkins

Gesendet: Donnerstag, 25. Juli 2013 um 18:22 Uhr
Von: a...@imtech.res.in
An: gmx-users@gromacs.org
Betreff: [gmx-users] unable to equilibrate pressure in npt

Dear gromacs users,
I know similar issues have been raised many times on the list but I am unable to
solve the problem so I am seeking your advice. I am trying to simulate a protein
in a dodecahedron box. The system size is ~30k atoms. I have followed the
methodology given in the lysozyme tutorial i.e. minimization, nvt, npt and
production. However the average pressure values after 5, 10, 20 ns of npt
equilibration are not coming close to the reference pressure i.e 1 bar when
using parrinello rahman. I checked the mailing list and tried using Berendson
and after 10 ns I get average pressure close to 1 (0.85). However when I switch
to parrinello rahman for production run the average pressure again goes far from
1. Can someone please help me with this? Here are the g_energy outputs from
equilibration (parrinello rahman, 20ns) and production run (10ns after
Berendson).

Pressure 0.0300644 0.38 134.243 1.57106 (bar)

Pressure -0.0405509 0.79 134.204 0.151638 (bar)

Can someone please help me with this?

Regards.
Amin.

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Aw: [gmx-users] Calculate interaction energy dynamically

2013-07-22 Thread lloyd riggs

 

You still might be able to with a static group, such that you pick 5 random ones, then the rest as a block (all lipids).  Your only problem may be if you define say 5 of 100 independent, then you would have to sum A-B plus A-all others, so more complicated, but its just a suggestion.

 

Stephan


Gesendet: Montag, 22. Juli 2013 um 12:20 Uhr
Von: "Davit Hakobyan" 
An: "gmx-users@gromacs.org" 
Betreff: [gmx-users] Calculate interaction energy dynamically

Dear Gromacs Users,

Is there a way in Gromacs to calculate the interaction energy between any two neighbor lipids dynamically? Since the neighbor lipids change over time in the trajectory file specifying a static energy groups in the input script will not help.

Is there a way to accomplish this?

One could use the g_select tool to define dynamic groups but again the energy file needs a predefined groups which probably makes the g_select tool useless in this case?

Any advice is greatly appreciated.

Thanks a lot in advance.
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Aw: Re: [gmx-users] How to calculate enthalpy

2013-07-19 Thread lloyd riggs

I thought about this reguaring solvation energy.  If you use a good water model, and make a secoundary index for solvent (ie Solvent2 atoms x-xn), the normal Gromacs energy extraction would allow you to just extract all energy between protein and solvent2.  I assume you could do some extreemly accurate solvation energy calculations this way, but the guassians for say 10-20 parallel runs of the same system would be much greater than say a protein-protein interaction.  I am sure solvent models would have to be good as well, but may allow you to do what you wished, however I would make sure through others first, and I do not know what you wished to do completly.

Stephan Watkins

Gesendet: Montag, 15. Juli 2013 um 19:25 Uhr
Von: "lloyd riggs" 
An: "Discussion list for GROMACS users" 
Betreff: Aw: Re: [gmx-users] How to calculate enthalpy

Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)?  And the energy of the internal structural hydrogen bonds that were disrupted?  Assuming no acidic enviornment where electrons are involved...means of coarse...

Gesendet: Montag, 15. Juli 2013 um 10:34 Uhr
Von: pooja_gu...@nccs.res.in
An: vvcha...@gmail.com, "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] How to calculate enthalpy

Thanks Vitaly

but how??

let's say the difference between unfolded to folded protein is 100 water
molecules. What is the correct procedure to calculate (theoretically) the
entrapy correspond to single water molecule for stabilizing/destabilizing
the protein.

help me

> Sure, you can.
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jul 15, 2013 at 8:38 AM,  wrote:
>
>> Hi
>>
>> I want calculate the enthalpy of water molecule corresponding to protein
>> folded and unfolded state.
>> How much a single water molecule (enthalpy and free energy) contribute
>> in
>> folding ?
>> Can we calculate enthapy from g_energy?
>>
>>
>>
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Aw: Re: [gmx-users] defining impropers necessary?

2013-07-17 Thread lloyd riggs


You can also look them up (angles bond distances) in the CRC handbook or online and just put the angle(distances direct into the .itp file for your ligand, as well as impropers...it works for all the force fields, unless you use hybrids (CH3=1 representation)...it comes out wierd as the different force fields put the same numbers different.  Such as distance 1.18, 118.0 to 1180.0 depending on representation is all...

 

Stephan

 

Gesendet: Mittwoch, 17. Juli 2013 um 19:33 Uhr
Von: "gromacs query" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] defining impropers necessary?

Dear Justin,

Thanks for reply and explanation, and..:

>> you've got an amide flanked by two methylene groups as the repeat unit
>> All the amino acids in the aminoacids.rtp file specify impropers
centered on the C and N atoms of the peptide bond.

I meant to say its easy to define (in general) impropers for chiral
centers, but not sure about bonds (here peptide). In oplsaa.ff I just
looked ALA in aminoacids.rtp for which there are two impropers.

ALA impropers:

-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y

which should be as follows:

H CH3 H
I I I
(-)C-N--CA--C---N(+)
I I I
O H O
^ ^ ^
^ ^ ^
[-C]-[ALA]---[N+]


Does this mean both improper terms are making peptide bond planar (two
peptide bonds: left side and right side of ALA), but in my case as you
noticed there are two methylene groups. So is it correct if I define
improper for my polymer as:

C C2 N H
C1 N C O


thanks

regards,
Jiom


On Wed, Jul 17, 2013 at 6:51 PM, Justin Lemkul  wrote:

>
>
> On 7/17/13 11:39 AM, gromacs query wrote:
>
>> Dear Justin,
>>
>> 1) I can understand the improper for stereocenters (chiral) easily but
>> with
>>
>
> OPLS doesn't use impropers for chiral centers.
>
>
> bonds I am confused (I have tried to explain below please let me know if I
>> have defined impropers correctly for peptide to keep it planar).
>>
>> H1 O H3
>> \ I /
>> --C1---C--N---C2--
>> / I \
>> H2 H H4
>>
>>
>>
> OK, funky text drawing :) But it looks like you've got an amide flanked
> by two methylene groups as the repeat unit.
>
>
> So I think improper (being zero) to keep peptide planar should be defined
>> (and sufficiently) as: O C N C1
>> and dihedral should be which is simple as: O C N H
>>
>> But it confuses me, why one needs to define improper for peptide. If I
>> just
>> keep dihedral angle strict (high force constant) then it will make peptide
>> freezed! so it will remain planar.
>>
>>
> The OPLS approach for amides is to define normal dihedrals as well as
> impropers. Keep in mind that rotations about a bond and out-of-plane
> bending are different types of motion. I suppose you could achieve what
> you're thinking of by very strong force constants for the dihedrals, but I
> would wonder if you're then throwing the balance of 1-4 interactions
> (especially charges) out of whack.
>
>
> 2) Also, I am not sure whether OPLS needs this peptide bond to be defined
>> with improper, someone have experienced this please suggest?
>>
>>
> All the amino acids in the aminoacids.rtp file specify impropers centered
> on the C and N atoms of the peptide bond. I would stick with that approach.
>
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | (410)
> 706-7441
>
> ==**
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Aw: Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread lloyd riggs

Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)?  And the energy of the internal structural hydrogen bonds that were disrupted?  Assuming no acidic enviornment where electrons are involved...means of coarse...
 

Gesendet: Montag, 15. Juli 2013 um 10:34 Uhr
Von: pooja_gu...@nccs.res.in
An: vvcha...@gmail.com, "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] How to calculate enthalpy

Thanks Vitaly

but how??

let's say the difference between unfolded to folded protein is 100 water
molecules. What is the correct procedure to calculate (theoretically) the
entrapy correspond to single water molecule for stabilizing/destabilizing
the protein.

help me

> Sure, you can.
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jul 15, 2013 at 8:38 AM,  wrote:
>
>> Hi
>>
>> I want calculate the enthalpy of water molecule corresponding to protein
>> folded and unfolded state.
>> How much a single water molecule (enthalpy and free energy) contribute
>> in
>> folding ?
>> Can we calculate enthapy from g_energy?
>>
>>
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Aw: [gmx-users] Figures of PCA analysis

2013-07-10 Thread lloyd riggs

There vectors.  Theres some good older papers explaining the whole thing from Van Gunstern, Berendsen, and some other good ones from de Groot that explain them well and includes combining them with other data analysis types, but I dont remeber the actual publications.  A few are in the mid 1990's, however these explain PCA better than some of the newer ones...but some extensive reading...or text books from van guntstern and/or Berendsen explain the whole thing well, from the math to the actual "what it means" aspect. 
 

Gesendet: Mittwoch, 10. Juli 2013 um 14:46 Uhr
Von: "Ahmet yıldırım" 
An: "Discussion list for GROMACS users" 
Betreff: [gmx-users] Figures of PCA analysis

Dear users,

I have a few questions about PCA analysis. I see the figures below in the most
of the publications:
1.) Figure:Eigenvalues along the eigenvectors
This figure gives contribution of eigenvalues along the eigenvectors to the
overall motion of the protein???
2.) Figure:the projection of the MD trajectories onto the first ten
principal components
This figure gives contribution of the first 10 eigenvectors to the overall
motion of the protein???
3.)The projection of the MD trajectories onto the plane of the first and
the second principal components
This figure gives knowledge about conformational spaces of structures???

Which one gives information about the motion of the structure?
Can anyone explain to me in detail what these figure are?
--
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Aw: [gmx-users] Umbrella sampling- force vs time plots

2013-07-09 Thread lloyd riggs

From running a bunch of these your pullf.xvg should look like a curve and taper off at the end (go down) or you didnt reach the maximum...with the force I had to play around and started with published work for similar proteins, but had to increase the force from 1000 (published) to 2000, so a large pull force (say 2500) and then looking at the pullf.xvg gives you the max peak, which you just set it slightly over this, mine was higher than published as the protein had more affinity, if you set it too low it just acts like a horminic oscillator...with the rate, I found if there is no force, only rate, it doesn't do anything pulling apart something with a high affinity, with a small molecule the pull rate worked (I only tried this a couple times)...somone may have better suggestions,

Stephan Watkins

Gesendet: Dienstag, 09. Juli 2013 um 18:56 Uhr
Von: rookie417
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling- force vs time plots

Hello all,

I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer over a distance
of 5nm:

pull=umbrella
pull_geometry=direction
pull_vec1=1 0 0
pull_start=yes
pull_ngroups=1
pull_group0=surf
pull_group1=poly
pull_rate1=0.01
pull_k1=1000

After the simulation, pullf.xvg plot I obtained is a linearly increasing
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
sure if this is right. My question is, on what basis do we select the
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
choice of parameters as long as the system does not deform? How does an
ideal force-time plot look like and does the choice of pull_k1 affect the
histogram? It appears, the entire procedure depends on the choice of input
of these two variables. I would greatly appreciate if someone can explain
this concept.

Thanks a lot.
Andy

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Aw: [gmx-users] Can't read 1048576 bytes of 'pullx500.xvg' to compute checksum.

2013-06-25 Thread lloyd riggs

I had this some time ago and cant remember everything, other than its a format problem. My end solution that worked was to simply cut and past in columns the entire pullf into one .xvg, say in gnumeric retaining an origional header, than read it into xmgrace, and then just write it out from xmgrace again to file xxx.xvg then it worked. I still could not find out why, and spent hours making sure everthing had same space numbers, or tab spacing, or etc...the only thing I noted was with xmgrace theirs a & or something at the end, but putting even this in manually to the files did not work...dont know if that helps...

Stephan

Gesendet: Dienstag, 25. Juni 2013 um 10:48 Uhr
Von: "Steven Neumann"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] Can't read 1048576 bytes of 'pullx500.xvg' to compute checksum.

Dear Users,

I know this error has been discussed many times but the outcome from
mdrun -pf and -px stopped at the same time which is 39470 ps. Somehow
gromacs caanot read pullx500.xvg but no clue why. I tried dos2gmx and still
the same error occur.

As I do not care about pullx500.xvg I run grompp again to change the tpr
file and set pull_nstxout = 0 then run from the checkpoint but then the
error occurs that 4 out of 5 files to append are only present.

Can you advise please?

Aw: Re: [gmx-users] Re:Problems with extending runs

2013-06-15 Thread lloyd riggs

I should add, one is an automated submit system, the others manual quing where you set parmeters (the ones that work), and the system is large around 90 120 90 angstrom box with around 170-180,000 atoms.  Still, the que output from the manual submission simply sets -nt 6, and the rest of the input as standard defaults.
 

Gesendet: Samstag, 15. Juni 2013 um 02:05 Uhr
Von: "lloyd riggs" 
An: "Discussion list for GROMACS users" 
Betreff: Aw: Re: [gmx-users] Re:Problems with extending runs



 
 
I have a bizzar problem.  I did 21 simulation for 4 ns each.  These were equ'd for 4ns prior, then taken from an assembly run over 4ns so between 300 pico and 4ns additional each.  A reviewer wants a couple extnded ends added,say like 4 extra ns, which I can only do 1-4 at most due to time limits (they take several days with 4-5 nodes, 8cpu quad core amd)  Now I just simply took the end run .mdp files, added these on, generated .tpr file, and a short check to generate a checkpoint .cpt.  I ran one on the cluster here in bern, one on a home PC and submitted one to the dutch/euro grid system.  The one on the grid in bern works fine, the one on my PC as well (intel 8 core), however it only reaches 75,000 of 20 million time steps necessary in 8 hours, I could never go beyonda 0.0005 time step (well 0.0008 but kept it at the former due to ease of changing file parmeters), any case, when I submit it to the Eu/dutch grid it crashes at at step 5000 with a PME, non-equilibrated error.  My question is why does it run on one, the exact same tpr tested, but not the other?

I looked at versions 4.5.5 my pc, 4.5.7 at unibe and a altered version of 4.5.3 on the dutch/eu grid.  Other than that, I can not find a problem, but woundered, as use of an extra que would have helped but most likely not now, as I have a response time.  I can not fathom why it would give such large changes however in bonds/angles in one but not the other as the versions are not that different?  Was there a large change between these versions, or other possibilities?

Stephan Watkins







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Aw: Re: [gmx-users] Re:Problems with extending runs

2013-06-14 Thread lloyd riggs

 
 
I have a bizzar problem.  I did 21 simulation for 4 ns each.  These were equ'd for 4ns prior, then taken from an assembly run over 4ns so between 300 pico and 4ns additional each.  A reviewer wants a couple extnded ends added,say like 4 extra ns, which I can only do 1-4 at most due to time limits (they take several days with 4-5 nodes, 8cpu quad core amd)  Now I just simply took the end run .mdp files, added these on, generated .tpr file, and a short check to generate a checkpoint .cpt.  I ran one on the cluster here in bern, one on a home PC and submitted one to the dutch/euro grid system.  The one on the grid in bern works fine, the one on my PC as well (intel 8 core), however it only reaches 75,000 of 20 million time steps necessary in 8 hours, I could never go beyonda 0.0005 time step (well 0.0008 but kept it at the former due to ease of changing file parmeters), any case, when I submit it to the Eu/dutch grid it crashes at at step 5000 with a PME, non-equilibrated error.  My question is why does it run on one, the exact same tpr tested, but not the other?

I looked at versions 4.5.5 my pc, 4.5.7 at unibe and a altered version of 4.5.3 on the dutch/eu grid.  Other than that, I can not find a problem, but woundered, as use of an extra que would have helped but most likely not now, as I have a response time.  I can not fathom why it would give such large changes however in bonds/angles in one but not the other as the versions are not that different?  Was there a large change between these versions, or other possibilities?

Stephan Watkins


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Fw: Aw: [gmx-users] Enthalpy Confusion

2013-06-12 Thread lloyd riggs

I appologise with the below, I got entropy and enthalpy confused for a mement. Funny.

Stephan

Gesendet: Dienstag, 11. Juni 2013 um 23:54 Uhr
Von: "lloyd riggs"
An: "Discussion list for GROMACS users"
Betreff: Aw: [gmx-users] Enthalpy Confusion

If you only want the total for the system or a delta for an entire run, indexed group there of, covarience (covar/aneig) does a good job. I found neither actually fit, but the covarience does, or if you do it by hand using only LJ parmeters for the indexed sets, however I was using proteins, so for the fluid system ?, but it took some publication look ups that were quite old. (well not that old 1980's)

Stephan

Gesendet: Dienstag, 11. Juni 2013 um 20:09 Uhr
Von: "Jeffery Perkins"
An: gmx-users@gromacs.org
Betreff: [gmx-users] Enthalpy Confusion

This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average or the
instantaneous values from g_energy switched over to SI so that there is no
issue there, the results are different (manual calculation is around 2x the
g_energy result).

So the question is, what am I overlooking in the analysis of the data i
have?

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Aw: [gmx-users] Enthalpy Confusion

2013-06-11 Thread lloyd riggs


If you only want the total for the system or a delta for an entire run, indexed group there of, covarience (covar/aneig) does a good job.  I found neither actually fit, but the covarience does, or if you do it by hand using only LJ parmeters for the indexed sets, however I was using proteins, so for the fluid system ?, but it took some publication look ups that were quite old. (well not that old 1980's)

 

Stephan

 

Gesendet: Dienstag, 11. Juni 2013 um 20:09 Uhr
Von: "Jeffery Perkins" 
An: gmx-users@gromacs.org
Betreff: [gmx-users] Enthalpy Confusion

This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average or the
instantaneous values from g_energy switched over to SI so that there is no
issue there, the results are different (manual calculation is around 2x the
g_energy result).

So the question is, what am I overlooking in the analysis of the data i
have?



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Aw: Re: [gmx-users] GPU problem

2013-06-04 Thread lloyd riggs

 

Thanks, thats exact what I was looking for.

 

Stephan


Gesendet: Dienstag, 04. Juni 2013 um 22:28 Uhr
Von: "Justin Lemkul" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] GPU problem



On 6/4/13 3:52 PM, lloyd riggs wrote:
> Dear All or anyone,
> A stupid question. Is there an script anyone knows of to convert a 53a6ff from
> .top redirects to the gromacs/top directory to something like a ligand .itp?
> This is usefull at the moment. Example:
> [bond]
> 6 7 2 gb_5
> to
> [bonds]
> ; ai aj fu c0, c1, ...
> 6 7 2 0.139 1080.0 0.139 1080.0 ; C CH
> for everything (a protein/DNA complex) inclusive of angles, dihedrials?
> Ive been playing with some of the gromacs user supplied files, but nothing yet.

Sounds like something grompp -pp should take care of.

-Justin

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Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE:[gmx-users] GPU problem

2013-06-04 Thread lloyd riggs

 

Dear All or anyone,

 

A stupid question.  Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp?  This is usefull at the moment.  Example:

 

[bond]

    6 7 2    gb_5

 

to

 

[bonds]

; ai  aj  fu    c0, c1, ...

  6  7   2    0.139  1080.0    0.139  1080.0 ;   C  CH  

 

for everything (a protein/DNA complex) inclusive of angles, dihedrials?

 

Ive been playing with some of the gromacs user supplied files, but nothing yet.

 

Stephan Watkins
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Aw: [gmx-users] Nose-Hover chains for membrane protein simulation

2013-06-02 Thread lloyd riggs

 

Off subject, I thought a good pop up for the end of file processing etc...would be

 

 ___
 "Government spies are everywhere, they're in your home, they're in your hair
 they're down the street and hiding in walls
 They're waiting to take you away" Fabulous flying freak brothers.

___

 

from the 60's 70's commic...

 

Stephan Watkins

 


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Aw: [gmx-users] Free energy calculation: merge the topology of 2 molecules

2013-05-30 Thread lloyd riggs

I've had 2 problems like this. 1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked,
there might be better suggestions though.

Stephan

Gesendet: Donnerstag, 30. Mai 2013 um 20:48 Uhr
Von: "Dejun Lin"
An: gmx-users@gromacs.org
Betreff: [gmx-users] Free energy calculation: merge the topology of 2 molecules

Hi all,

I'm trying to set-up a free energy calculation where a molecule has +2
charge in it's native state (state A) and no charge in the mutant (state
B). Since the molecule has net +2 charge, I have to add counter-ions to
neutralize the system in state A. But in order to transform it to state B
and still maintain a neutral system, the counter-ions have to be
transformed too. I tried only transforming only the target molecule not the
ions but the simulation crashes very quickly.

I searched the gmx-users archives and found some suggestion about merging
the topology definition of ions into that of the molecule under one
[moleculetype] section. I tried that but mdrun warned me with tons of
"inconsistent shift":

There were 2 inconsistent shifts. Check your topology
There were 18 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
There were 12 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
...

and the simulation can't be run in parallel because mdrun would just quick
and complain about not being able to do domain decomposition:

There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 29.6188 nm

I guess the issue is Gromacs thinks those counter-ions belongs chemically
to the target molecule although they are actually not in close proximity in
space, which mess up the DD. partition.

I wonder if there's a way to get around that.

Thanks,
Dejun
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Aw: [gmx-users] umbrella sampling for two polymer interaction

2013-05-30 Thread lloyd riggs


Dear Jiom,

 

Look at justines tutorial, there's example pull .mdp.

 

Stephan Watkins

 

Gesendet: Donnerstag, 30. Mai 2013 um 14:44 Uhr
Von: "gromacs query" 
An: "Discussion list for GROMACS users" 
Betreff: [gmx-users] umbrella sampling for two polymer interaction

Dear All,

I want to do Umbrella sampling between two different polymers (A and B)
interacting with each other with starting configuration separated by some
distance and I am trying to bring them closer.

I have some queries regarding pull inputs: (this is for to run a umbrella
sampling at some distance)

pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = ???
pull_ngroups = 2?
pull_group0 = polymer_B
pull_group1 = polymer_A
pull_init1 = 0
pull_rate1 = 0.0


please suggest for following:

1) pull_dim I have set to Y Y Y: Is this correct I do not want to make
it interact with some directional vector

2) Which should be group0 or group1, in other words should I pull both
together or how I should decide which one should be reference and
which to be pulled as both are different polymers?

3) And also what should be pull_ngroups because if there is no
reference group then it should be 2

4) I am not able to understand pull_start option with pull_init1. In
this case if it is set to yes and 0.0 respectively then does that mean
this combination is equivalent to pull_start = No if I just assume
pull_init1 does not have any default value (which is 0.0); not
existing

5) Also finally where are upper and lower bounds defined. pull_k1 =
1000 is harmonic applied to some equilibrium distance value. How this
distance is taken by the programme (or it is just the starting
distance taken between two groups) and what are the +/- values
defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is
assumed equilibrium value and r1 is lower and r4 is upper value which
defines shape of potential)


thanks,

Jiom
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Aw: Re: Re: [gmx-users] GPU-based workstation

2013-05-28 Thread lloyd riggs

Dear Dr. Pali,

Thank you,

Stephan Watkins

Gesendet: Dienstag, 28. Mai 2013 um 19:50 Uhr
Von: "Szilárd Páll" 
An: "Discussion list for GROMACS users" 
Betreff: Re: Re: [gmx-users] GPU-based workstation

Dear all,

As far as I understand, the OP is interested in hardware for *running*
GROMACS 4.6 rather than developing code. or running LINPACK.

To get best performance it is important to use a machine with hardware
balanced for GROMACS' workloads. Too little GPU resources will result
in CPU idling; too much GPU resources will lead to the runs being CPU
or multi-GPU scaling bound and above a certain level GROMACS won't be
able to make use of additional GPUs.

Of course, the balance will depend both on hardware and simulation
settings (mostly the LJ cut-off used).

An additional factor to consider is typical system size. To reach near
peak pair-force throughput on GPUs you typically need >20k-40k
particles/GPU (depends on the architecture) and throughput drops below
these values. Hence, in most cases it is preferred to use fewer and
faster GPUs rather than more.

Without knowing the budgdet and indented use of the machine it is hard
to make suggestions, but I would say for a budget desktop box a
quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a
fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.
If you're considering dual-socket workstations, I suggest you go with
the higher core-count and higher frequency Intel CPUs (6+ cores >2.2
GHz), otherwise you may not see as much benefit as you would expect
based on the insane price tag (especially if you compare to an i7
3939K or its IVB successor).

Cheers,
--
Szilárd

On Sat, May 25, 2013 at 1:02 PM, lloyd riggs  wrote:
> More RAM the better, and the best I have seen is 4 GPU work station. I can
> use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8
> or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> though with GPU's, as on a board there packed, so extra cooling things may
> help not blow a GPU, but I would look for good ones (ask around), as its a
> video game market and they go for looks even though its in casing? The
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the
> price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad is
> also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> software, not Gromacs, so would be nice to see performance...for a small 100
> atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent
> eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps
> eq's
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" 
> An: "Discussion list for GROMACS users" 
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attributes of
> MB should be taken into account for best performance on such multi-gpu
> station ?
>
> James
>
> 2013/5/25 lloyd riggs 
>
>> There's also these, but 1 chip runs 6K US, they can get performance up to
>> 2.3 teraflops per chip though double percission...but have no clue about
>> integration with GPU's...Intell also sells their chips on PCIe cards...but
>> get only about 350 Gflops, and run 1K US$.
>>
>> http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
>> http://www.xilinx.com/
>>
>> They can design them though to fit a PCIe slot and run about the same, but
>> still need the board, ram etc...
>>
>> Mostly just to dream about, they say you can order them with radiation
>> shielding as well...so...
>>
>> Stephan Watkins
>>
>> *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
>> *Von:* "J

Aw: Re: Re: [gmx-users] GPU-based workstation

2013-05-25 Thread lloyd riggs

 

You can also look at profilling on varied web sites, the high end Nvidia run only slightly better than the 2 year old ones, from an individual point not worth the money yet, but if you have the money? as I've been browsing.

 

Also, the sim I did on the cluster was 180-190,000 atoms so the exact same performance the other person had.

 

Stephan


Gesendet: Samstag, 25. Mai 2013 um 15:19 Uhr
Von: "James Starlight" 
An: "Discussion list for GROMACS users" 
Betreff: Re: Aw: Re: [gmx-users] GPU-based workstation

Richard,

thanks for suggestion!

Assuming that I'm using 2 high end GeForce's what performance be better

1) in case of one i7 (4 or 6 nodes ) ?

2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core

What properties of MB should take into account primarily for such
Xenon-based system. Does such MBs support multi-GPU ( I noticed that many
such MBs lack for PCI)?

James

2013/5/25 Broadbent, Richard 

> I've been running on my Universities GPU nodes these are one E5-xeon
> (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms
> of DMF under NVE. The performance has been a little disappointing
> ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get
> 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2
> quad-core xeon processors I get 30-40ns/day.
>
> I think that to achieve reasonable performance the system has to be
> balanced between CPU's and GPU's probably getting 2 high end GPU's and a
> top end xeon E5 or core i7 would be a good choice.
>
>
> Richard
>
> From: lloyd riggs >
> Reply-To: Discussion users 
> gmx-users@gromacs.org>>
> Date: Saturday, 25 May 2013 12:02
> To: Discussion users >
> Subject: Aw: Re: [gmx-users] GPU-based workstation
>
> More RAM the better, and the best I have seen is 4 GPU work station. I
> can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8
> or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> though with GPU's, as on a board there packed, so extra cooling things may
> help not blow a GPU, but I would look for good ones (ask around), as its a
> video game market and they go for looks even though its in casing? The
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the
> price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad
> is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> software, not Gromacs, so would be nice to see performance...for a small
> 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
> solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say
> 50 ps eq's
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" 
> jmsstarli...@gmail.com>>
> An: "Discussion list for GROMACS users" 
> gmx-users@gromacs.org>>
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attributes of
> MB should be taken into account for best performance on such multi-gpu
> station ?
>
> James
>
> 2013/5/25 lloyd riggs >
>
> > There's also these, but 1 chip runs 6K US, they can get performance up to
> > 2.3 teraflops per chip though double percission...but have no clue about
> > integration with GPU's...Intell also sells their chips on PCIe
> cards...but
> > get only about 350 Gflops, and run 1K US$.
> >
> > http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
> > http://www.xilinx.com/
> >
> > They can design them though to fit a PCIe slot and run about the same,
> but
> > still need the board, ram etc...
> >
> > Mostly just

Aw: Re: Re: [gmx-users] GPU-based workstation

2013-05-25 Thread lloyd riggs

 

Id go for the i7 6 core,

 

To the other message, funny.  I bought ATI's as they clock faster and cost 1/3 the price of Nvidia's but then the software all went to Nvidia.  The new ATI with twice the shaders runs at the same speed (around 1-1.3 terflops ) due to the same problems the Nvidias ran into with IO (or maybe onboard RAM does solve the problem if they went up to 16 or 32 MB)  Gromacs, etc...doesn't run on ATI's, and I've been hoping they, AMD,  catch up, but all I ever see is the constant in 6 months then nothing.

 

I ran around 40 4 ns simulations on University blades with 8 AMD quad cores, using 3 blades I only was able to get 1 ns/day, but never pressed it as far as why so slow, as I needed to finish.  With the Nvidia at  even 5 ns/day I or alot of people could do some really nice work as far as publishing, with raw data in 2 weeks time, so now I feel a bit saddened...

 

I also just found openCL profilling with CUDA 5 that will take any C or C++ software, and mark all sections you need to convert to openCL, but the trial software is 30 day, then 250 US$...

 

Stephan


Gesendet: Samstag, 25. Mai 2013 um 15:19 Uhr
Von: "James Starlight" 
An: "Discussion list for GROMACS users" 
Betreff: Re: Aw: Re: [gmx-users] GPU-based workstation

Richard,

thanks for suggestion!

Assuming that I'm using 2 high end GeForce's what performance be better

1) in case of one i7 (4 or 6 nodes ) ?

2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core

What properties of MB should take into account primarily for such
Xenon-based system. Does such MBs support multi-GPU ( I noticed that many
such MBs lack for PCI)?

James

2013/5/25 Broadbent, Richard 

> I've been running on my Universities GPU nodes these are one E5-xeon
> (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms
> of DMF under NVE. The performance has been a little disappointing
> ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get
> 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2
> quad-core xeon processors I get 30-40ns/day.
>
> I think that to achieve reasonable performance the system has to be
> balanced between CPU's and GPU's probably getting 2 high end GPU's and a
> top end xeon E5 or core i7 would be a good choice.
>
>
> Richard
>
> From: lloyd riggs >
> Reply-To: Discussion users 
> gmx-users@gromacs.org>>
> Date: Saturday, 25 May 2013 12:02
> To: Discussion users >
> Subject: Aw: Re: [gmx-users] GPU-based workstation
>
> More RAM the better, and the best I have seen is 4 GPU work station. I
> can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8
> or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> though with GPU's, as on a board there packed, so extra cooling things may
> help not blow a GPU, but I would look for good ones (ask around), as its a
> video game market and they go for looks even though its in casing? The
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the
> price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad
> is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> software, not Gromacs, so would be nice to see performance...for a small
> 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
> solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say
> 50 ps eq's
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" 
> jmsstarli...@gmail.com>>
> An: "Discussion list for GROMACS users" 
> gmx-users@gromacs.org>>
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attrib

Aw: Re: [gmx-users] GPU-based workstation

2013-05-25 Thread lloyd riggs


More RAM the better, and the best I have seen is 4 GPU work station.  I can use/have used 4.  The GPU takes 2 slots though, so a 7-8 PCIe board is really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot board really holds 8 or 10 GPU's).  There's cooling problems though with GPU's, as on a board there packed, so extra cooling things may help not blow a GPU, but I would look for good ones (ask around), as its a video game market and they go for looks even though its in casing?  The external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont know performance wise, the onboard GPU, the more RAM the marrier...so yes, normal work stations you can get 4 GPU's for a 300 US$ board, but then the price goes way up (3-4000 US$ for an 8-10 gpu board).  RAM ordered abroad is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests software, not Gromacs, so would be nice to see performance...for a small 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10 minutes real  for 1 ns sim, but tried simple large 800 amino, 25,000 solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps eq's

 

Stephan

 

Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
Von: "James Starlight" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] GPU-based workstation

Dear Dr. Watkins!

Thank you for the suggestions!

In the local shops I've found only Core i7 with 6 cores (like Core
i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
than with 4 cores in case of i7 cpu (assuming that I run simulation in
cpu+gpu mode )?

Also you've mentioned about 4 PCeI MD. Does it means that modern
work-station could have 4 GPU's in one home-like desktop ? According to my
current task I suppose that 2 GPU's would be suitable for my simulations
(assuming that I use typical ASUS MB and 650 Watt power unit). Have
someone tried to use several GPU's on one workstation ? What attributes of
MB should be taken into account for best performance on such multi-gpu
station ?

James

2013/5/25 lloyd riggs 

> There's also these, but 1 chip runs 6K US, they can get performance up to
> 2.3 teraflops per chip though double percission...but have no clue about
> integration with GPU's...Intell also sells their chips on PCIe cards...but
> get only about 350 Gflops, and run 1K US$.
>
> http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
> http://www.xilinx.com/
>
> They can design them though to fit a PCIe slot and run about the same, but
> still need the board, ram etc...
>
> Mostly just to dream about, they say you can order them with radiation
> shielding as well...so...
>
> Stephan Watkins
>
> *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
> *Von:* "James Starlight" 
> *An:* "Discussion list for GROMACS users" 
> *Betreff:* [gmx-users] GPU-based workstation
> Dear Gromacs Users!
>
>
> I'd like to build new workstation for performing simulation on GPU with
> Gromacs 4.6 native cuda support.
> Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
> and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
> with SD integrator)
>
>
> Now I'd like to build multi-gpu wokstation.
>
> My question - How much GPU would give me best performance on the typical
> home-like workstation. What algorithm of Ncidia GPU integration should I
> use (e.g SLI etc) ?
>
>
> Thanks for help,
>
>
> James
> --
> gmx-users mailing list gmx-users@gromacs.org
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Aw: [gmx-users] GPU-based workstation

2013-05-24 Thread lloyd riggs

There's also these, but 1 chip runs 6K US, they can get performance up to 2.3 teraflops per chip though double percission...but have no clue about integration with GPU's...Intell also sells their chips on PCIe cards...but get only about 350 Gflops, and run 1K US$.

http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor

http://www.xilinx.com/

They can design them though to fit a PCIe slot and run about the same, but still need the board, ram etc...

Mostly just to dream about, they say you can order them with radiation shielding as well...so...

Stephan Watkins

Gesendet: Freitag, 24. Mai 2013 um 13:17 Uhr
Von: "James Starlight"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] GPU-based workstation

Dear Gromacs Users!

I'd like to build new workstation for performing simulation on GPU with
Gromacs 4.6 native cuda support.
Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
with SD integrator)

Now I'd like to build multi-gpu wokstation.

My question - How much GPU would give me best performance on the typical
home-like workstation. What algorithm of Ncidia GPU integration should I
use (e.g SLI etc) ?

Thanks for help,

James
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Aw: Re: [gmx-users] the "-dist" flag of g_hbond tool

2013-05-24 Thread lloyd riggs


 

The hydrogen bonding energy would have/is usefull to myself.  An example, I use the .ndx as you did below for protein-protein interactions only.  I get around 25 and 28 for two different states.  The interesting part is the 25 is about 7 times the delG, however the hydrogen bonds move much less, and remain in contact longer across the trajectory.  A nice hydrogen bonding energy (real Vs. Calculated) would have added a nice graph to make a point.

 

Sincerely,

 

Stephan Watkins

 

Gesendet: Freitag, 24. Mai 2013 um 16:04 Uhr
Von: "Erik Marklund" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] the "-dist" flag of g_hbond tool

It used to be. I didn't realise it was still in the code. We experimented a bit with having a continuous bond criterion instead of a binary measure. It didn't do for us what we hoped it would so it was abandoned. I know that some people are using Espiniozas empirical formula for bond energy, however, so that code may be resurrected at some point.

Erik

On 24 May 2013, at 15:12, CHEN Pan  wrote:

> Yes. I have looked at it already. I may need to spend time to understand
> it.
>
> By the way, in the source code, it seems some part are written for
> calculating hydrogen bonding energy, but I haven't see any "flag command"
> could give a output of "hydrogen bonding energy" file. Is it still under
> development?
>
>
> 2013/5/24 Erik Marklund 
>
>> Hm. That is peculiar. The source code has the answer of course. I can have
>> a look next week to see why that is.
>>
>> Erik
>>
>> On 24 May 2013, at 14:11, CHEN Pan  wrote:
>>
>>> Hi,
>>>
>>> I have 512 donors and 1024 acceptors.
>>>
>>> I have just tested "g_hbond" with my standard crystal structure, which I
>>> should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
>>> hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
>>> that the summation of population is 200.
>>>
>>>
>>> 2013/5/24 Erik Marklund 
>>>
 Hi,

 See below

 On 24 May 2013, at 11:45, CHEN Pan  wrote:

> Dear Gromacs users,
>
> I am confused about the g_hbond tools.
>
> 1) When I use "-dist" to get the distribution of hydrogen bonding
 distance,
> I found that the summation of the population is always 200 (the
>> y-column
> below). I am not sure if it's was done with normalization or not, if
>> yes,
> the summation should be one, if no, then the summation should equals to
 the
> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
> have 440 hydrogen bonds. Why here is always 200, not matter what types
>> of
> hydrogen bonds.

 How many donors do you have, and how many acceptors?

>
> 2) In my system, there are several different types of hydrogen bonds,
 such
> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
> bonds. Is there any "smart" way to separately calculate those hydrogen
> bonds? By using the "index.ndx" file, I could separate the intra-chain
> hydrogen bonds, then I can get the inter-chain ones using the total one
> minus the intra-chain one. It may be possible to do the same for the
> intra-sheet and the inter-sheet. However, this strategy seems
>> "complex".
> Did anybody have experience or ideas for this problem?
>
> Pan
>
> # This file was created Fri May 24 11:06:01 2013
> # by the following command:
> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b
>> 11000
 -e
> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
> #
> # g_hbond is part of G R O M A C S:
> #
> # Gromacs Runs One Microsecond At Cannonball Speeds
> #
> @ title "Hydrogen Bond Distribution"
> @ xaxis label "Hydrogen - Acceptor Distance (nm)"
> @ yaxis label ""
> @TYPE xy
> 0.0025 0
> 0.0075 0
> 0.0125 0
> 0.0175 0
> 0.0225 0
> 0.0275 0
> 0.0325 0
> 0.0375 0
> 0.0425 0
> 0.0475 0
> 0.0525 0
> 0.0575 0
> 0.0625 0
> 0.0675 0
> 0.0725 0
> 0.0775 0
> 0.0825 0
> 0.0875 0
> 0.0925 0
> 0.0975 0
> 0.1025 0
> 0.1075 0
> 0.1125 0
> 0.1175 0
> 0.1225 0
> 0.1275 0
> 0.1325 0
> 0.1375 0
> 0.1425 0
> 0.1475 0
> 0.1525 0
> 0.1575 0
> 0.1625 0
> 0.1675 0
> 0.1725 0
> 0.1775 0
> 0.1825 0
> 0.1875 0
> 0.1925 0
> 0.1975 0
> 0.2025 0
> 0.2075 0
> 0.2125 0
> 0.2175 0
> 0.2225 0
> 0.2275 0
> 0.2325 0.00538632
> 0.2375 0.125501
> 0.2425 1.23562
> 0.2475 6.08295
> 0.2525 16.4279
> 0.2575 28.6597
> 0.2625 36.0576
> 0.2675 35.154
> 0.2725 28.1539
> 0.2775 19.8073
> 0.2825 12.4602
> 0.2875 7.23832
> 0.2925 4.06577
> 0.2975 2.15794
> 0.3025 1.14423
> 0.3075 0.588366
> 0.3125 0.310611
> 0.3175

Aw: [gmx-users] GPU-based workstation

2013-05-24 Thread lloyd riggs


Dear Dr. Starlight,

 

Dont know the answere to all, but funny I was looking at performance on varied others web sites.  I use a core i7 970, but it seems their newest chip is almost the same as the i7 in performance (thier newer chips dont scale past 12 cores for some internal chip based design, they put out a 60 core chip for 1K and it doesnt even reach 1 terflop), and the newer GPU's suffer from board IO limits due the PCIe being maxed out.

 

As far as boards, home PC (im in Switzerland so have been mind distroyed as far as prices), there's a 4 CPU 10 GPU tyan board for 4K US (if you dig enough maybe 3,500) which with ram, chips and a single Nvidia would run up to 5-6 K US$.  The i7 970's can be baught for 30-50 US$ a pop now if you look becuase intel overshot its abilities and gave off the rights to several bulk manufacturers (all LG 1366 socket chips even i5's) as they add more pins (2100 or something), but you have to spend a day or two on the internet looking through sellers abroad.  The Nvida's are the pricy thing, however from what I have read, you dont get much more from their latest as well as mentioned, so 2 more years waiting, or something like I mentioned with a 2 year old Nvidia or two, would be the best especially for research purposes.  Otherwise a single 300 US board with 4 usable PCIe's (ASUS arnt bad), ram, 1 i7 970, and 1 Nvida from 2 years back gives you around 1.3 terflops, with their lates 1.4-1.5 teraflops (integrated use of chip alone).  The i7 I have I have got around 350 Gflops for some things with 8 threads.  I use radeons though, although this requires user programming, and if you use ther FFT libraries, you have to sign your first child over and loose any freeware redistribution rights in any way, otherwise their supposedly supposed to have all the same CUDA like libraries by the end of the summer (Portlandgroup , openCL), but I heard the same for 2 years now.

 

Sincerely,

 

Stephan Watkins

 

Gesendet: Freitag, 24. Mai 2013 um 13:17 Uhr
Von: "James Starlight" 
An: "Discussion list for GROMACS users" 
Betreff: [gmx-users] GPU-based workstation

Dear Gromacs Users!


I'd like to build new workstation for performing simulation on GPU with
Gromacs 4.6 native cuda support.
Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
with SD integrator)


Now I'd like to build multi-gpu wokstation.

My question - How much GPU would give me best performance on the typical
home-like workstation. What algorithm of Ncidia GPU integration should I
use (e.g SLI etc) ?


Thanks for help,


James
--
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Aw: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables

2013-05-22 Thread lloyd riggs

 

Dear Andrish Reddy,

 

Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the "forcefieldX/SPC.itp" or equivalent section so it doesn't loop, but dont know if it works in your case.  Just a quick suggestion to try, as I parse e-mails.  Smone else probably has better answeres though...

 

Stephan


Gesendet: Mittwoch, 22. Mai 2013 um 16:09 Uhr
Von: "Andrish Reddy" 
An: gmx-users@gromacs.org
Betreff: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables

Greetings,

I am trying to use tabulated potentials for the VdW interactions between
TIP5P water molecules.
I have tested my topology file to make sure that it gives reasonable results
with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,
C12=4*eps*sig^12. I am able to match the energies with an identical run not
using look-up tables. The problem comes when I want to include the C6 & C12
parameters within the table. This is needed for dealing with more complex
multi-parameter potential functions.

I tried testing this with the standard Lennard-Jones potential. Setting
g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my
table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)]

I set vdw-type = user in my mdp file and modified my topology so that:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 yes 0.5 0.8333

[ atomtypes ]
; name at.num mass charge ptype C6 C12
OW_tip5p 8 16.00 0. A 1.0e+00 1.0e+00

Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg
and C6=4*eps*sig^6 , C12=4*eps*sig^12
The run proceeds fine with no warnings or errors, but the LJ and Potential
energies are an order of magnitude higher than when using the standard
table. I don't understand why I am not able to reproduce the results by this
method?

Thanks,
Andrish




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Aw: Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-18 Thread lloyd riggs

 

Or just do it by hand and replace the lines in the .top with each protein chains .itp file.

 

Stephan


Gesendet: Freitag, 17. Mai 2013 um 16:17 Uhr
Von: "Mark Abraham" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] Expanding a .top file to have all connection information

How does grompp -pp look?

Mark


On Fri, May 17, 2013 at 3:40 PM, davidjrosenman wrote:

> Hello everyone,
>
> This may be a bit out of the purview of this list, but it can't hurt to
> ask.
>
> Let me start from the beginning: I'm trying to take a structure/topology
> that I generated with GROMACS tools and convert it to run with NAMD. The
> problem is that this is a huge simulation box with many different atom
> types
> (homodimeric protein, water, lipids, ions), and I am having a lot of
> trouble
> generating a .psf file from the information I have.
>
> The current strategy I'm pursuing to accomplish this task is to use the
> top2psf script:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/
>
> The issue is that this script will only read what is explicitly written in
> the top file. All of the include records will be ignored, as will multiple
> molecules. So, the output is a psf suitable ONLY for the first chain of my
> dimer. I want a psf that will include all components of my structure,
> including the lipids, waters, etc.
>
> So, I ask, is there a way to expand a topology to explicitly get all of the
> connectivities in a structure? I figure this information must be contained
> in the .tpr file, but that's neither human readable nor compatible with
> top2psf.
>
> If you have any advice for that, or for the larger problem at hand, I would
> appreciate it. Thank you very much!
>
> Cheers,
> David Rosenman
> Grad Student, Rensselaer Polytechnic Institute
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Expanding-a-top-file-to-have-all-connection-information-tp5008345.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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Aw: Re: [gmx-users] air-water-interface

2013-05-14 Thread lloyd riggs

I was under the impression a vacumn, or even gas/liquid interface becomes uniform molecule wise in such simulations due to scale.  Thus, the applied pressure and other corrections necessary to set up the interface on a small scale, such as caclulated force at an imaginary interface for given gas/liquid systems?  I wounder though, is it possible to give the pressure corrections a direction (a single wall instead of the entire unit cell)?
 

Gesendet: Montag, 13. Mai 2013 um 14:16 Uhr
Von: "Nawel Mele" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] air-water-interface

Thanks a lot for your answer.
So by increasing the z coordinate after solvated the system we induce
creation of a empty space above the solvated box.
After minimisation a few water molecules move above its new empty space
because their link are not strong enough.


2013/5/13 Justin Lemkul 

>
>
> On 5/13/13 8:01 AM, Nawel Mele wrote:
>
>> So we just compute an interface vacuum-water like the picture in attach in
>> increase the coordinate value of the z-axis of the box?
>>
>
> The list does not accept attachments. If you want to post an image or
> file, provide a public link to access it.
>
>
> BUt I don't understand how just like that we creat an empty place and
>> water
>> move to this place??
>>
>>
> Seems like intuitive behavior to me. Think about basic physics and
> thermodynamics.
>
> -Justin
>
>
>>
>> 2013/5/13 Justin Lemkul 
>>
>>
>>>
>>> On 5/13/13 6:10 AM, Nawel Mele wrote:
>>>
>>> Hi all,

 I am performing a simulation of protein at air/water interface.

 For create an air-water interface I just expand the box in the z
 direction.
 So,aAfter minimization we can noticed that water molecules moved out of
 bulk water in the z direction.

 Why you just need to expand the z-axis for obtain this interface?? I
 don't
 understand the mechanism.


 You're not creating an air-water interface by doing this, you're
>>> creating
>>> an vacuum-water interface and your water molecules are evaporating into
>>> the
>>> empty space.
>>>
>>> -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
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
>>> gmx-users mailing list gmx-users@gromacs.org
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>>> >
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>>> >
>>>
>>>
>>
>>
>>
>>
>>
> --
> ==**==
>
> 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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--
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Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
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Aw: Re: [gmx-users] PCA_RMS fluctuation per residue?

2013-05-09 Thread lloyd riggs

You should make a good index file and read the options in g_covar and g_anaeig in the manual and just the command line help. I found the new builds of Gromacs allows indexing after a long trajectory, but did not know this before hand. I had tried it with older versions, a couple years back, but it complained about wrong index groups set...so dont know if it was a fix or somthin else on my side from older to newer versions.

Gesendet: Mittwoch, 08. Mai 2013 um 08:25 Uhr
Von: "Tsjerk Wassenaar"
An: "Discussion list for GROMACS users"
Betreff: Re: [gmx-users] PCA_RMS fluctuation per residue?

Hi Rajiv,

Square the values, sum them per residue and take the square root.

Cheers,

Tsjerk

On May 8, 2013 7:24 AM, "라지브간디" wrote:

Dear gmx users,

I've done covariance matrix for backbone of protein using g_covar command.

Also, can able to plot all projections through g_anaeig.

However, I could only able to do -rmsf: plot the RMS fluctuation per atom
of eigenvectors BUT i wants to do them per residue? How can i achieve this?

In manual it shows -filt: command filter the trajectory to show only the
motion along eigenvectors. How i do visualize this kind of motions?

Rajiv

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Aw: Re: [gmx-users] Proteins with ADP & ATP cofactors

2013-05-07 Thread lloyd riggs

That works, wish you could choose more force fields in the anti-chamber as a plugin. There's some auxillary scripts also for martini and gromos force fields to .psf but they were mostly for the ff19, so partial atom. They antichamber is probably easier, and if you get something in ff19 (or better 22 as an all atom) you just have to add a few missing hydrogens for the first, etc...the problem I had was the naming schemes go from simple numbers (listed say as angles 1-4-3) to deffinitions, (CA-C-H) so easy to make mistakes...

Stephan Watkins

Gesendet: Dienstag, 07. Mai 2013 um 01:03 Uhr
Von: "micheal j twin"
An: gmx-users@gromacs.org
Betreff: Re: [gmx-users] Proteins with ADP & ATP cofactors

Dear Stephan,
thank you for your reply.

I'm performing some test with antechamber for a de-novo parametrization,
hope to see some good results with it.

> You probably have to do a hand job. Look at the .itp/top files and then
the force field parmeters, here's not many atoms, so it would take only a
couple hours.
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Aw: [gmx-users] Proteins with ADP & ATP cofactors

2013-05-04 Thread lloyd riggs

You probably have to do a hand job. Look at the .itp/top files and then the force field parmeters, there's not many atoms, so it would take only a couple hours.

Stephan Watkins

Gesendet: Freitag, 03. Mai 2013 um 12:36 Uhr
Von: "micheal j twin"
An: gmx-users@gromacs.org
Betreff: [gmx-users] Proteins with ADP & ATP cofactors

Dear all,
Does anybody have the parameters files for ATP and ADP for the AMBER03 ff?

Alternatively, I know that I can find the corresponding files on the AMBER
package web-site

http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

but I don't know how convert these files so I can use them with GROMACS.

There are several emails on this mailing-list concerning my request, but I
can't find a reply which clearly address the problem.

Thank you
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Aw: [gmx-users] Re: how is the pulling force measured

2013-04-30 Thread lloyd riggs

I appologise, I meant defined at the same time without complaining, not just either direction.
 

Gesendet: Montag, 29. April 2013 um 22:23 Uhr
Von: "lloyd riggs" 
An: "S. Watkins" 
Betreff: Aw: [gmx-users] Re: how is the pulling force measured



 
 
Dear All,

Doing a water/temp energy minimization just for a figure with a large molecule that has several connected parts, I ran into a bizzar question.

So I found its possible by accident to define improper dihedrails forwards and backwards without gromacs complaining, such as atom 1 2 3 4 and 4 3 2 1.  My question is, if your topology has this, does it affect the calculations (angle energy or other)?

 

Stephan Watkins







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Aw: [gmx-users] Re: how is the pulling force measured

2013-04-29 Thread lloyd riggs

 
 
Dear All,

Doing a water/temp energy minimization just for a figure with a large molecule that has several connected parts, I ran into a bizzar question.

So I found its possible by accident to define improper dihedrails forwards and backwards without gromacs complaining, such as atom 1 2 3 4 and 4 3 2 1.  My question is, if your topology has this, does it affect the calculations (angle energy or other)?

 

Stephan Watkins


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Aw: Re: [gmx-users] Estimations of the drug's affinity

2013-04-15 Thread lloyd riggs

You can also embed your protein-bound small molecule, protein unbound small molecule a good distance away in solvent of choice, then eq it at the proper temp/pressure.  Then take several samples along an equed space, let them just run unrestrained, and you can calculate the energy change mean...same technique as the tutorial munus the pulled aspect.  I posted something like this in response to a question Justin answered in a similar way, basically a single value with error estimates is generated, you have an A and B state with no in-between, with no energy curve, ie alot of work but single value.  Since I posted this, I realized there are several older 1990's papers that did similar things, and there are large effects on the final affinity from simple solvent changes (salts/ions concentraition, other solvent molecules)...

Gesendet: Sonntag, 14. April 2013 um 13:24 Uhr
Von: "Justin Lemkul" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] Estimations of the drug's affinity

On 4/14/13 2:13 AM, James Starlight wrote:
> Dear Gromacs users!
>
> I wounder to know if it possible to simple estimate drug affinity by mean
> of MD simulation? As I know the drug's property is based on the free energy
> change of bound-unbound ligand. So It seems that Justin's tutorial (free
> energy calculations) might be usefull if it would not be so routine for the
> drugs ( in that workflow several coulombic-vdw interactions must be
> uncoupled). Is there any more easily way to perform such calculations for
> the typical small-drug compounds consisted of several non-covalent
> interactions with the receptors ?
>

Free energy calculations require considerable effort. You can approach the task
in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc. There is a large
body of literature detailing methods for such calculations.

-Justin

--

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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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Aw: Re: [gmx-users] MD publications

2013-04-08 Thread lloyd riggs


Sorry, I tried posting this once but it was spammed or something.  In any case, are there any suggestions for mostly MD based journals (publication wise as content), a favorites or something if somone wanted to turn it into that,

 

Stephan Watkins
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Aw: [gmx-users] Re: Simulating a large system

2013-04-08 Thread lloyd riggs

Funny, I thought of a large Ribosome system. You can in vacuo already with an i7 or AMD equivalent EM a 600 amino acid system with a 12-15A solvent shell in an hour to three using the CPU alone. Thats from test of Gromacs and a non-eq'd system. so about 1 work day to get through NPT. Thus, I doubt there is much problem even using the whole system for most things if your time frame is a day or two and newer PC .

Stephan Watkins

Gesendet: Montag, 08. April 2013 um 11:35 Uhr
Von: "Juan Antonio Raygoza Garay"
An: vvcha...@gmail.com
Cc: gmx-users@gromacs.org
Betreff: [gmx-users] Re: Simulating a large system

Sure, it's basically improving minimization time. if i can focus all my resources in simulating or minimizing a portion of the system while ignoring other parts that are too far away from the selected portion, it can also be possible to run some simulations without the need of a big cluster and sort of obtaining about the same results. This goes to my interest of harnessing small computing systems for doing all these tasks. There are systems like rna molecules where i could get the fine grained structure first and then running the entire molecule to obtain the coarser structure.

As someone says it might not improve time but at least having the ability to run portions only on my small desktop overnight or just leave it there running a lot of this could be accomplished. I do have access to a cluster but having to wait in the queue is time that can be used to getting somewhere, maybe slower but you're moving.

On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote:

> Vitaly Chaban

Aw: [gmx-users] Re:Concept

2013-04-05 Thread lloyd riggs

 
So last week I read a post about liquid/gas layers in a box and it has me thinking (ie I cant shut it off).  As it would sim wise (and I asume there is already something somewhere that does it) for a large body of fileds such as astrophysics, liquid dynamics, gas/gas interface I woundered if anyone had thoughts on the subject.

 

It was pointed a standard box, say 200 nm cubed with half liquid, half gas or vacum quickly just diffuses the molecules across the area.  My thoughts were you could introduce a wall, with a set filed parameter in the mid point which would correct for some of the things happening.  I think now, a box would also have to be irregular for such things, ie 200x200x2000 or some extreem deminsion in one axis.  The point would be to do expirements say where I have a set atmosphere of several gases at a given pressure, etc...then introduce a solvent to half the box, ie just h2o, and then simulate the changes to this system in general to a final equilibrated point.  The main feature say I take 4 gases, CO2, NH3, O2, N2, and Ar or Ne, etc... The varied solubility of these is something like 3.5 g/L, 5 g/L , 0.02 g/L, etc... thus drastic effects on the atmospheric side of the box.  The delima is at the molecular level, there is a gas/liquid interface that in the real world is not to pretty to model, mostly acting like 3-5 layers of mixing as far as equilibrim dynamics are conscerned over a macroscopic level of only 1-2 uM, but at the sim level this deminsion is enourmous.  Thus I would to the developers propose a wall table set that may help reduce the sizes concerned.  I should aslo add for Astrophysics type things, say the earth atmosphere, at the extreem altitudes, you have layering of gases, Vs. Mixing of these below a specific altitude, or conversly density from pressure and garvity (close to the surfaces of the planet, but mostly applicable to large atoms such as Radon or Ar).  These higher areas are a few 100 meters to few feet, but behave like a liquid liquid interface.  This is increasingly important to fields modeling foreighn atmospheres, examples like Jupiter or a far off planet where you can get the mixture percentages and density, but need to then model these based in size and mass would be say 10K ATM, and an area where gravity or not begin to play a roll.

 

Thaughts suggestions, etc...would be intersting.  Or grants for somone...

 

Sincerely,

 

Stephan Watkins

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Fw: Aw: Re: [gmx-users] Re: density profile

2013-04-02 Thread lloyd riggs

Sorry, meant to post this on the bb.

Gesendet: Dienstag, 02. April 2013 um 11:50 Uhr
Von: "lloyd riggs" 
An: vvcha...@gmail.com
Betreff: Aw: Re: [gmx-users] Re: density profile

How would you set up a gas/gas interface, say modeled after a large gas planet or upper atmosphere, without effects from garvity and pressures in the 10K plus ATM?  In such a system the gases behave almost like liquids, but most effects are from extreems of conditions.  Actaul interfaces though I assume would include large amounts of mixing right at the atomic level interface, but I have no clue how far this would extend.  If you remove rotational effects, I am willing to bet you can model a gas/gas interface at the atomic level with extreem conditions, which might be an aset in some fileds/areas of research.  Minus gravitational effects though, I do not know if they could work properly.  You can however set up a ligid gas interface by introducing box systems with differences in force at a plain across the midpoint equal to gas/liquid interfaces, or gradients of force, etc...but in all cases I assume a minimal amount of programming might be necessary.  Opinions/answers anyone?

Stephan Watkins

Gesendet: Montag, 01. April 2013 um 20:43 Uhr
Von: "Dr. Vitaly Chaban" 
An: Elisabeth , gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re: density profile

There is a wonderful data page devoted to methane in wikipedia...

It follows from this webpage that you will get a perfect density profile if
you decrease your T down to 150K...

On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban wrote:

>
>
>
> On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth  wrote:
>
>> You are right. I compressed my alkane system under NPT at 400 K at 100
>> bar. The normal boiling point is below 425 K. So it seems there in no way
>> one can obtain profiles obove boiling point of liquid given than with the
>> current NVT recipe molecules tend to fill up the free zone no matter how
>> much pressure was applied in the previous NPT runs?
>>
>>
>
> You cannot get a profile just because you have NO LIQUID and NO INTERFACE
> upon these conditions. Gas fills all the available space, there is no such
> thing as gas/gas interface.
>
> And yeah... Forget about NPT and learn the Gibbs phase rule.
>
>
> Dr. Vitaly Chaban
>
>
>
>
>
>
>>
>> On 1 April 2013 14:22, Dr. Vitaly Chaban  wrote:
>>
>>>
>>>
>>>
>>> On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth  wrote:
>>>
>>>> Hi Vitaly,
>>>>
>>>> The problem was with cpt file since it re sets the last line of gro. I
>>>> removed the -f flag and now the Z direction is extended. However, I see
>>>> that molecules tend to fill up the upper zone (free space) rapidly. I am
>>>> wondering how I can obtain the density profile if I am going to get another
>>>> uniformly distributed box after this NVT run?
>>>>
>>>>
>>>
>>> Here we come to the question what your system is composed of... Based on
>>> the density profile, this is not a (conventional) liquid... Polymer,
>>> non-Newtonian liquid ... or what?
>>>
>>> If molecules tend to fill vacuum, it can only mean that the matter you
>>> are simulating is above critical point.
>>>
>>> What is your T and what are the particles in your box?
>>>
>>>
>>> Dr. Vitaly Chaban
>>>
>>>
>>>
>>>
>>>>
>>>> I am expecting to see how density changes with Z at the solvent -vacuum
>>>> interface
>>>>
>>>> Please advise me on this,,
>>>>
>>>> Thanks!
>>>>
>>>>
>>>> On 1 April 2013 13:14, Dr. Vitaly Chaban  wrote:
>>>>
>>>>> I think if you use checkpoint files, the program does not read either
>>>>> MDP, or GRO, or TOP, or anything except CPT.
>>>>>
>>>>>
>>>>> Dr. Vitaly Chaban
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth wrote:
>>>>>
>>>>>> Hi vitaly,
>>>>>>
>>>>>> The initial structure is indeed extended but the final output.gro is
>>>>>> not. I think its because I am using the cpt file from the previous NPT runs
>>>>>> as input for the new runs? Do I have to remove the -t flag?
>>>>>>
>>>>>>
>>>>>> On 1 April 2013 12:47, Dr. Vitaly Chaban  wrote:
>>>>>>
>>>>>>> Hi Eli

Aw: [gmx-users] Re: Re: help with chromophore of a GFP

2013-03-25 Thread lloyd riggs

If you back the origional papers alot of the conversions can be found. I dont know the papers off the top of my head,

so you should just ask your PI, collegues or the board. They are a pain, one paper will have 2 and be missing one definition you want, etc...

Stephan Watkins

Gesendet: Montag, 25. März 2013 um 16:56 Uhr
Von: "Anna MARABOTTI"
An: gmx-users@gromacs.org
Betreff: [gmx-users] Re: Re: help with chromophore of a GFP

Dear gmx-users,

I'm still dealing with my problem of obtaining
parameters for my chromophore of the GFP family, in order to treat it as
a new residue. I'm trying (VERY hardly) to add missing parameters into
ffbonded.itp file for AMBER99SB ff, using those parameters found in
files calculated by Antechamber. To date, I've added those parameters
related to bonds, now I have to add those related to angles, dihedrals
and impropers.

I'm dealing with section [angletypes] of file
ffbonded.itp, and I'm looking at the values of cth (that I imagine is
the angle force constant expressed in kJ mol^-1 rad^-2, correct?) I see
that all parameters in ffbonded.itp are multiple of the value of 4.184,
corresponding to the conversion factor between kcal and kJ. If I divide
each of these values, I obtain a value corresponding to a number such as
80, 70, 120, 40 etc. Instead, if I look at those corresponding values
found using Antechamber, I see, as expected, numbers with decimals, that
are often very different from those present in ffbonded.itp (when I
compare angles present in both files). For example, for the angle
CT-CT-CT (3 C sp3), I see in ffbonded.itp a value of cth equal to 334.72
kJ mol^-1 rad^-2. For the same angle, Antechamber calculated a value of
63.21 kcal/mol^-1 rad^-2. If I do 334.72/4.184 the result is 80, which
is different from the value of Antechamber. If I consider the angle
CT-CT-HC (2 C sp3 and one H) the angle force constant in Antechamber is
46.37 kcal mol-1 rad-2, in ffbonded.itp is 418.4, that divided by 4.184
is exactly 100.

Moreover, the same values of angles and forces are
applied to angles that in my opinion are quite different among them. For
example, I found the same value of 109.5 (th) and 418.4 (cth) for:
H2-CT-N*, H1-CT-N*, H1-CT-OH, H1-CT-OS, H2-CT-OS, N*-CT-OS, C-CT-H1,
H1-CT-N2, C-CT-HC... All these angles involve atoms that seem very
different to me, and I'd expect to find different values of these
parameters.

It seems to me that values into ffbonded.itp related to
these force constants are quite "strange", especially for the fact that
they are EXACTLY multiple of 4.184, and I wonder if I'm correctly
interpreting these values.

Best regards

Anna

Re: [gmx-users] help with chromophore of a GFP

2013-03-21 Thread lloyd riggs

I had problems having not used gromacs in years a couple years ago.  Try 
running it through with the output as a pdb from pdb2gmx, cut off all headers, 
and you can then just compare the two files in gedit emacs or word and see 
differences.  That might help.  I routinely just keep everything in pdb format 
as its easier than jumping back and forth.


 Original-Nachricht 
> Datum: Thu, 21 Mar 2013 21:43:16 +0100
> Von: Mark Abraham 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] help with chromophore of a GFP

> On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI 
> wrote:
> 
> >
> >
> > Dear Mark,
> >
> > thank you for your message. I'm happy to be on the
> > right track; unfortunately the end point seems to be very far away...
> >
> >
> > I tried to obtain that CFY hydrogens and protein hydrogens are all
> > matching the aminoacids.rtp entry, in order to avoid dealing with
> > aminoacids.hdb. This is what I did:
> >
> > - starting from the pdb file of
> > the protein, I removed CFY entry (prot_noCFY.pdb)
> >
> > - I used pdb2gmx to
> > add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb
> > -p topol.top
> >
> > - I inserted CFY_H.pdb (obtained with Pymol in a previous
> > passage in which I added H with Pymol to the protein, including CFY)
> > into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb.
> >
> > In this way, H atoms
> > bound to "regular" residues have been added using Amber99SB, therefore
> > they are compatible with this ff, and atoms of CFY (previously added
> > with Pymol) have the same naming convention in aminoacids.rtp (that I
> > edited using atom types, charges etc. calculated with Antechamber on
> > this molecule coming from Pymol). Obviously, the atom numbering is not
> > sequential: the last atom of V63 (the last "regular" residue before CFY)
> > is numbered 938, the first atom of H68 (the first "regular" residue
> > after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1
> > to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not
> > the same as in the coordinates of CFY (I adapted the sequence of atoms
> > following the format of other residues in aminoacids.rtp), the numbering
> > of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but
> > disordered (19-54-20-55...49-50-24-25).
> >
> 
> Seems fine. pdb2gmx is mostly about atom/residue naming. grompp is mostly
> about atom/residue/moleculetype ordering.
> 
> - At this stage, I used
> > pdb2gmx again to create the topol.top file with all coordinates correct:
> >
> >
> > pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top
> >
> >
> > (selecting amber99sb forcefield and tip3p for water, as recommended
> > option)
> >
> > This is the message error from pdb2gmx:
> >
> > Read 'FLUORESCENT
> > PROTEIN', 3346 atoms
> > Analyzing pdb file
> > Splitting PDB chains based on
> > TER records or changing chain id.
> > There are 1 chains and 0 blocks of
> > water and 218 residues with 3346 atoms
> >
> >  chain #res #atoms
> >  1 'A' 213
> > 3346
> >
> 
> I'd be concerned about the difference in residue count here, but 4.5.4 is
> so old I've no idea whose fault this is.
> 
> 
> > All occupancies are one
> > Opening force field file
> > ./amber99sb.ff/atomtypes.atp
> > Atomtype 1
> > Reading residue database...
> > (amber99sb)
> > Opening force field file
> > ./amber99sb.ff/aminoacids.rtp
> > Residue 94
> > Sorting it all out...
> > Opening
> > force field file ./amber99sb.ff/dna.rtp
> > Residue 110
> > Sorting it all
> > out...
> > Opening force field file ./amber99sb.ff/rna.rtp
> > Residue
> > 126
> > Sorting it all out...
> > Opening force field file
> > ./amber99sb.ff/aminoacids.hdb
> > Opening force field file
> > ./amber99sb.ff/dna.hdb
> > Opening force field file
> > ./amber99sb.ff/rna.hdb
> > Opening force field file
> > ./amber99sb.ff/aminoacids.n.tdb
> > Opening force field file
> > ./amber99sb.ff/aminoacids.c.tdb
> >
> > Processing chain 1 'A' (3346 atoms, 213
> > residues)
> > There are 327 donors and 319 acceptors
> > There are 539 hydrogen
> > bonds
> > Will use HISE for residue 22
> > Will use HISD for residue 38
> > Will use
> > HISE for residue 62
> > Will use HISE for residue 68
> > Will use HISD for
> > residue 109
> > Will use HISE for residue 119
> > Will use HISE for residue
> > 172
> > Will use HISH for residue 193
> > Will use HISH for residue 197
> > Will use
> > HISE for residue 217
> > Identified residue SER3 as a starting
> > terminus.
> > Identified residue SER218 as a ending terminus.
> > 8 out of 8
> > lines of specbond.dat converted successfully
> > Special Atom Distance
> > matrix:
> >  MET9 MET11 MET15 HIS22 HIS38 MET41 MET47
> >  SD110 SD149 SD232
> > NE2317 NE2549 SD596 SD700
> >  MET11 SD149 0.807
> >  MET15 SD232 2.279 1.627
> >
> > HIS22 NE2317 3.707 2.983 1.466
> >  HIS38 NE2549 1.401 0.928 2.127 3.254
> >
> > MET41 SD596 1.458 0.665 1.144 2.384 1.001
> >  MET47 SD700 3.059 2.324 0.995
> > 0.801 2.656 1.761
> >

Re: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)

2013-03-10 Thread lloyd riggs


I can imagine why you would go past the first few, but does it print the zero's 
or just negate them from the equation, as there 0?

Stephan
 Original-Nachricht 
> Datum: Sun, 10 Mar 2013 14:34:52 -0500
> Von: Hyuntae Na 
> An: "gmx-users@gromacs.org" 
> Betreff: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for
> l-bfgs)

> Dear, This is the same issue that I asked last time. I wonder (1) if I
> setup the test wrong, (2) if NMA *can* have smaller than 6 eigenvalues even
> though the conformation of a protein is in equilibrium  in the enough degree,
> or (2) if it gromacs does not make it in equilibrium because of the limit
> of the tolerance that gromacs can take care of. Is there anyone who can
> give me an advice for this? I updated the sample location in the case that the
> previous Skype link is not available. I am studying several protein
> fluctuation proteins using NMA (Normal Mode Analysis). In the mean time, I 
> found
> out in many cases that NMA hessian matrix has about 3-4 zero eigenvalues
> even though having 6 zero eigenvalues are expected. I tried to reduce the
> tolerance level lesser than 10^-6 for the l-bfgs minimization, but still it
> have only 4 zero eigenvalues. Following is the 9 smallest eigenvalues (you
> can see that it has only 4 close-to-zero eigenvalues):
> -1.8476593e-06-1.2164109e-06-1.4830436e-071.3104790e-061.1364704e+001.7418209e+002.2836573e+003.7218206e+004.4875873e+00
> Theoretically, NMA should have 6 zero eigenvalues which represents the
> freedom of the rotation and translation. I wonder why this happens.
>  
> Is there anyone who can help me for this problem?
>  
> In order to specify the case, I leave a link to download a zip file that
> contains files for one NMA tests having the problem: script, mdp, pdb, gro,
> topol, etc. The zip file also includes the eigenvalue/vector files.
> http://129.186.69.109/NMA-test.zip
>  
> Thank you very much.
>  
> -- Hyuntae
>   
>   -- 
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Re: [gmx-users] GROMACS 4.6.1 released

2013-03-06 Thread lloyd riggs


Dear All,

I had a quick 2 questions, 1) does anyone know (as a long whiles back I looked 
over CUDA code not the CUDA Gromacs) if there is more than just obtaining the 
specs for an ATI GPU within Gromacs (explanation:For CUDA alone it appeared all 
you needed was an elaborate definition in the CUDA libraries for devices which 
broke down to deminsions of the arrays, etc as they are arranged wire/signal 
wise.  I looked at these and they were much larger than expected, but free from 
CUDA and ATI) within Gromacs 

and 2) Does anyone know if its legal to just post such a thing as the legal 
issues of using CUDA and ATI are pretty complex, or should this be directed 
elsewhere?  I do know its legal to do it yourself, I just dont know if its 
legal to share such things.

Sincerely,

Stephan Watkins

 Original-Nachricht 
> Datum: Tue, 5 Mar 2013 20:14:47 +0100
> Von: Mark Abraham 
> An: Discussion list for GROMACS users , 
> gmx-annou...@gromacs.org
> Betreff: [gmx-users] GROMACS 4.6.1 released

> *Hi GROMACS users,
> 
> GROMACS 4.6.1 is officially released. It contains numerous bug fixes, some
> simulation performance enhancements and some documentation updates. We
> encourage all users to upgrade their installations from 4.6.
> 
> You can find the code, manual, release notes, installation instructions
> and
> test
> suite at the links below.
> 
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.1.tar.gz
> ftp://ftp.gromacs.org/pub/manual/manual-4.6.1.pdf
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.1.x
> http://www.gromacs.org/Documentation/Installation_Instructions
> http://gromacs.googlecode.com/files/regressiontests-4.6.1.tar.gz
> 
> Happy simulating!
> 
> The GROMACS development team*
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Re:Gromacs auxillary tools ideas

2013-03-02 Thread lloyd riggs


Dear All,

I read a paper by Van der Groot and realized some tool regarding simple 
paersons r values, or correlation co-efficient by different names would be a 
great analytical asset for macromolecular biology.  Looking over the code, 
g:sham seems to have begun implicating such things but it loos like a caotic 
mess.  Basically, I used gnumeric, but MS excel also has functions, and you can 
take say a PC analysis, and run any other data set and see if it "Correlates", 
ie is an effect of or not related in any way too some other factor, in the case 
of PC, energy versus anything else.  All they need is say you take your 
Gaussian 10-300 trajectories as a mean in a spread sheet (ie 200-5000) data 
points in a column, and compare it with PC (or any other thing you want, 
although energy is about the most comprehensive), and it gives a linear 
correlation based on pearsons two column correlation of relation (circa 
1895)...it does allow say for a a PC, then taking several things like distance, 
hydro
 gen bonding means between 2 prtoeins, domain distance, inter protein 
movements, inter protein hydrogen bonding, LJ or coloumb, etc... and tells you 
which is the energy or correlation...would be a great asset...

And any competent programmer namless could do it in a week or two...as a 
gromacs tool...would add Bio more to funding sources...

Sincerely,

Stephan Watkins
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Re: [gmx-users] GROMOS54A8 parameters in GROMACS format

2013-02-14 Thread lloyd riggs

Dear Stephane Abel,

Theres a link I on the gromacs web site to ATB, or you can google it.  If it is 
not in Gromacs format you can just write a couple 6 liner scripts to re-format 
it by parsing into the gromacs format,

Stephan Watkins

 Original-Nachricht 
> Datum: Wed, 13 Feb 2013 21:25:33 +
> Von: ABEL Stephane 175950 
> An: "gmx-users@gromacs.org" 
> Betreff: [gmx-users] GROMOS54A8 parameters in GROMACS format

> Hello all, 
> 
> Does somebody know where i can find  the latest GROMOS force field (i.e.
> GROMOS54A8) described in [1]  in the GROMACS format (gromos54a7.ff) ? 
> 
> [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247−1264 doi:
> http://pubs.acs.org/doi/citedby/10.1021/ct300156h
> 
> Thank you
> 
> Stephane
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[gmx-users] Re:Energy landscapes

2012-11-29 Thread lloyd riggs


Dear All,

I remember a post in the last couple months but cant find it.  In any case, by 
searching through van der groot et alls. papers, the -xmin, -xmax, -dim and 
-ngrid options third point, example: -xmin 3 3 3 -xmax 3 3 3 is for reading in 
the output 3d (projections on V1, V2, V3 or first three vectors, and is output 
as xyz points in a pdb file.  This can be read into various ploting or even 
pymol/vmd to illustrate the projection on a PCA of 3 dimensions.  From the lit 
it is supposed to show 2 or more conformational states, and a number of 
intermediary states in between (overall just a 3d PCA graph).  If I am wrong 
please correct me, but this is what the output for me was doing, and I 
personally prefer the 2D, as its easier to illustrait (as images in 3d lack the 
necessary rotation to show everything in a static image).

Sincerely,

Stephan Watkins
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Re: [gmx-users] Re:Ka/Kd

2012-11-11 Thread lloyd riggs

Dear Justin,

Thanks, Just a normal delta G then.  I wondered if it also was doing a matrices 
from 2 columns if you supply something like just the 2d output from 
covar/anaeig (PCA).  I did find a simple python 6 liner for just doing PCA with 
the first (or any 2) derivatives just using numpy, and some module written by 
tsjerk Wassenaar posted a few years ago (a Gromacs plugin called g_entropy) 
which all together seem to meet my needs.  Also (the above person) has a number 
of small python scripts for Gromacs for matirces, PCA, and just turning .xpm 
data from g_sham into a number matrices to put into a plotting tool (such as 
Scidavis or something).  There on a web page, and a few dozen just scattered in 
older gromacs postings.

If I had a request for Gromacs dev though it would be to multithread the vector 
portions of the analytical tools.  A single Intel i7 or AMD only uses one of 
the 8 cores, so it takes several hours, for each component times each of 
however trajectories are looked at.  Most everything else is a minute or two 
only using a single core.

Sincerely,

Stephan Watkins

 Original-Nachricht 
> Datum: Fri, 09 Nov 2012 14:44:31 -0500
> Von: Justin Lemkul 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:Ka/Kd

> 
> 
> On 11/9/12 1:02 PM, lloyd riggs wrote:
> > Dear All,
> >
> > Reguarding a question I asked below.  Does anyone know what the
> formulei, etc...are for g_sham taking in 2 columns (or 3 with time) and 
> turning it
> into a density matrix.  Is it just a count, summation on x-y or other?
> >
> 
> Values are divided into histograms and calculated by dG = -RT ln (P - P0),
> where 
> P0 is the histogram bin with the largest probability such that the value
> of dG 
> is set to zero here and all other values are relative to it.
> 
> -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:Ka/Kd

2012-11-09 Thread lloyd riggs

Dear All,

Reguarding a question I asked below.  Does anyone know what the formulei, 
etc...are for g_sham taking in 2 columns (or 3 with time) and turning it into a 
density matrix.  Is it just a count, summation on x-y or other?

Stephan Watkins

 Original-Nachricht 
> Datum: Thu, 08 Nov 2012 11:46:32 +0100
> Von: "lloyd riggs" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:Ka/Kd

> 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
> > > 
> > > ==

Re: [gmx-users] Re:Ka/Kd

2012-11-08 Thread 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
> > 
> > 
> > -- 
> > 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] Re:Ka/Kd

2012-11-06 Thread lloyd riggs

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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[gmx-users] Re:Ka/Kd

2012-11-05 Thread lloyd riggs

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)...

any words, etc are appreciated.

Stephan Watkins
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Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible

2012-10-06 Thread lloyd riggs

Could you explain to me how this would effect your domain decomposition?


 Original-Nachricht 
> Datum: Fri, 05 Oct 2012 23:05:33 -0400
> Von: Justin Lemkul 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re: Error There is no domain decomposition for 6 
> nodes that is compatible

> 
> 
> On 10/5/12 5:19 PM, Sonia Aguilera wrote:
> > Thank you a lot,
> >
> > I only changed the couple-intramol setting (couple-intramol=yes) and now
> > it´s running just fine. However I have a doubt about something. In the
> > manual says the following when using couple-intramol=no
> >
> > "In this manner the decoupled state of the molecule corresponds to the
> > proper vacuum state without periodicity effects"
> >
> > I don´t understand the real effects and implications of this on my
> > simulation. Does it mean that it is better to run with
> couple-intramol=no? I
> > also read that using couple-intramol=yes has it's advantages: "This can
> be
> > useful for partitioning free-energies of relatively large molecules,
> where
> > the intra-molecular non-bonded interactions might lead to kinetically
> > trapped vacuum conformations. Again, I don't understand what is the real
> > meaning of that. Can you please make this clear for me?
> >
> 
> Consider what (de)coupling means.  You are manipulating the interactions
> of a 
> chosen molecule with its surroundings as a function of lambda.  If you
> tell 
> mdrun that your calculation should not couple intramolecular interactions 
> (couple-intramol = no) then what that is saying is that all nonbonded 
> interactions within that given molecule are always calculated at full
> strength. 
>   That is what the manual is telling you - the calculation implies that 
> intramolecular terms are always on, as if the molecule were in a vacuum. 
> If you 
> do couple intramolecular interactions (couple-intramol = yes), then any 
> nonbonded interactions within your molecule of choice are also scaled as a
> function of lambda.  This may be beneficial for large molecules, since if
> you 
> are not coupling intramolecular interactions, you may get unnaturally
> strong 
> interactions within the solute molecule since the interactions with the 
> surrounding solvent are weakened as a function of lambda.  Thus you can
> get odd 
> geometries that get trapped and are detrimental to your sampling.
> 
> -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] Error There is no domain decomposition for 6 nodes that is compatible

2012-10-05 Thread lloyd riggs



you have to play with the ratio usually of domain decompositions Vs. Grid size, 
I had that error some time ago though, if you look at the generated .mdp from 
the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and 
play with it.  It dosent like odd numbers or non-whole decompositions which are 
based on the cpu's versus total size.

fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0

I might have remembered the answer wrong though, but someone will correct me if 
I am wrong I hope.

PS, are you from LA.  Just asking I used to know someone with the exact same 
name, but I also vaguely remember seeing your name here and asking that once 
before...

Stephan Watkins

> I am performing a free energy calculation based on Justin Lemkul's
> tutorial.
> My system is a protein in water and dodecane and I'm coupling the protein
> considering none to only vdw interactions for my lambda 0 and 1 states.
> However, I get this error when trying to minimize the system:
> 
> Fatal error:
> There is no domain decomposition for 6 nodes that is compatible with the
> given box and a minimum cell size of 7.55833 nm min1.0.mdp
>   
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> 
> I know I can fix easily this problem by using -nt 1 option. But I still
> want
> to use all available cores. I suspect the error is in the mdp file because
> if I use the following mdp file for the minimization it works. 
> 
> title   =  cpeptide
> cpp =  /usr/bin/cpp
> define  =  -DFLEX_SPC
> constraints =  none
> integrator  =  steep
> dt  =  0.002; ps !
> nsteps  =  1000
> nstlist =  10
> ns_type =  grid
> rlist   =  1.0
> rcoulomb=  1.0
> rvdw=  1.0
> ;
> ;   Energy minimizing stuff
> ;
> emtol   =  1000.0
> emstep  =  0.01
> 
> Obviously this mdp file does not work for free energy calculations. I
> still
> want to use the attached one, but I don´t know what to change to make it
> work.
> 
> This is the link for my log and mdp file.
> mdp_and_log_files.zip
>   
> 
> Thank you in advance, 
> 
> Sonia Aguilera
> Graduate Assistant
> Universidad de los Andes-Colombia
> 
> 
> 
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/Error-There-is-no-domain-decomposition-for-6-nodes-that-is-compatible-tp5001648.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Re: vmd-l: Re: compiling VMD with gcc 4.7

2012-10-04 Thread lloyd riggs


Dear All,

I spent two days converting a .top file from gromos53a6 to one readable by 
VMD/NAMD.

Now I am about to begin the ffbonded/nonbonded to a readable format for the 
same and would like to know beforehand if anyone has already done this so I can 
just use the library?  Most are straightforward conversions of format.  The 
main prblem is the NAMD (I believe) does not already have the parameters for cg 
or merged CH croups.  The gromos force fields for gromacs only do this with 
chain non-polar, leaving the charged H groups alone.  I did find however, no 
equivalent with trying to first generate a .psf file, and then looking at the 
vdw /angle, dihedrals and non bonded files for NAMD.

Example a methyl is CH3 with a mass of 15.00 CH2 Mass 14 ,etc  with only 3 atom 
type changes, you would think it wouldnt be so painfull, but it turns into a 
hellish nightmare.

Any links or pointers would be appreciated, however I already assume I have to 
do this myself to use the VMD tools with Gromacs traj.  Its still shorter than 
3 months of simulations with a new index file.

Sincerely,

Stephan Watkins
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[gmx-users] RE: Gromacs 2 CHARMM

2012-10-02 Thread lloyd riggs


Dear All,

Does anyone have a small script for converting Gromacs (GROMOS type) ff to 
CHARMM format, or an amino acid top file in CHARMM format for such.  I have 
seen some scripts, but they work only with different topology types.  Thought I 
would ask, otherwise I sit here for three days playing with text editors,

Sincerely,

Stephan Watkins
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Re: [gmx-users] DNA orientation restrain

2012-10-01 Thread lloyd riggs

Dear Dudu Tong

Theres a paper on using limited x y z restraints but I have forgotten it.  In 
any case theres a way to generate 1 2 or 3D positional restraints with just the 
grompp , and you can cut and past.  The output posre in the help command will 
give you a file, and theres a selection for what force you want applied , but 
If you want only 1 or 2 dimensions you just need a spread sheet editor, and can 
change 1 or 2 manually after they are generated.

Stephan Watkins

 Original-Nachricht 
> Datum: Mon, 1 Oct 2012 13:44:20 +0800
> Von: "仝督读" 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] DNA orientation restrain

> Hi everyone,
> 
> I am doing a DNA simulation in a long simulation box (the lengthen of z is
> much larger than x and y). So I want to constrain the DNA molecule lying
> along the z axis. But I don't know how to realize this in GROMACS.
> 
> Actually I notice there is orientation restraints in 4.3.5 of GMX Manual.
> But the orientation value is set to be observables of NMR experiments,
> such
> as this example:
> ; ai aj type exp. label alpha const. obs. weight
> 31 32 1  1  3  3  6.083  -6.73  1.0
> But how can I set the observable in my case as it's not an NMR experiment?
> 
> Any suggestion will be appreciate.
> Thanks very much
> 
> Dudu Tong
> <31%2032%201%201%203%203>
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Re: [gmx-users] Regarding RMSD analysis result

2012-09-24 Thread lloyd riggs

You can also just quickly visualize it in VMD and see if anything your looking 
at is not centred properly.  If it isnt you just have to centre it.

Stephan

 Original-Nachricht 
> Datum: Mon, 24 Sep 2012 04:32:33 -0700
> Von: naga sundar 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Regarding RMSD analysis result

> Dear justin
> 
>Thanks for ur suggestions
> 
>  While speaking about periodic conditions, I followed
> the similar condition for both native and mutant complexes. For native
> complexes not any big deviation was observed. So its confirmed that
> nothing
> wrong with periodic conditions. Since all the three mutations were having
> high clinical significance, we assuming mutation is the only reason for
> this abnormal RMSD behavior.  Sudden big increase in the RMSD was observed
> in previous mutational  MD studies.
> http://www.sciencedirect.com/science/article/pii/S0006291X08020792.
> 
> Overall, all  the factors are supporting our results. So shall we take
> this
> RMSD analysis as good result . Even after repeating the 20 ns MD
> simulation
> two times i got the same results.
> 
> 
> 
> 
> 
> 
> 
> 
> On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul  wrote:
> 
> >
> >
> > On 9/24/12 6:24 AM, naga sundar wrote:
> >
> >> Dear gromacs users
> >>
> >>  We performed MD simulation analysis for native and mutant
> >> models of protein-protein complexes. From 20 ns simulation trajectory,
> we
> >> generated RMSD graph for one native and three mutant complexes. For
> native
> >> complex in the entire simulation period, we observed  a constant RMSD
> >> (~0.15 to ~ 0.25 nm). But, three mutant complexes
> >> showed drastic fluctuation in theRMSD  (~0.15 to ~1.75) plot. We
> analysed
> >> all the 3D structure's in the fluctuated areas observed destruction of
> >> protein complexes.
> >> All the three mutants were already experimentally analyzed and reported
> >> that they are involved in the destruction of protein-protein
> interactions.
> >>
> >> Query 1: What may be the reason for sudden rise and fall of the RMSD
> >> values
> >> in mutant complexes. We are assume its because of the involvement of
> >> mutation.
> >> Query 2: Is there may any other reasons for drastic fluctuation in the
> >> RMSD
> >> Query 3: Observed results are rite.
> >>
> >> Here  iam attaching the RMSD graph for your observation.
> >>
> >>
> >>
> > Attachments to the list do not work.  You will have to post a link to a
> > file sharing site if you wish to share an image.
> >
> > Such jumps in RMSD are very suspect.  Since you are dealing with
> > protein-protein complexes, accounting for periodicity can be very
> > challenging.  Have you properly fit the trajectory such that your
> protein
> > subunits are not jumping across periodic boundaries?  If they are, then
> > your results are nothing more than an artifact.  If they are not, then
> you
> > have something more interesting, but a tenfold increase in RMSD is very
> > peculiar.
> >
> > -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
> >
> > ==**==
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> >
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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> 
> 
> -- 
> Regards
> N.NagaSundaram
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Re: [gmx-users] Analysis of enssemble of MD trajectories

2012-09-20 Thread lloyd riggs

Dear Dr.

I might be wrong, but I think you can use g_rms with two seperate trj files, 
and it takes the rms from the starting structure of the first one.  In which 
case you would have to decide which is the reference, and then just do it three 
times.

Theres also auxiliarry software which has plugins for this, such as VMD, Pymol, 
or even O run in some sort of batch.  In pymol I know it can be run as a 
script, but you need all saved pdb files extracted from each trj, so would be a 
bit large and pain.  with the VMD it has plugins for them, but I only played 
with it once.  If you only want to look at beginning and end rms from say the 
start and end for all traj-using just a couple pdb at either end would be easy 
in pymol and O.

There is also these new tools I found in Bio R (its called Bio3D if you look on 
the web for the freeware) , which are all scripts that I tried once, which work 
as well, mostly the take a reference structure and parse the pdbs output from a 
trj (if you write out each individually) but there values are different but 
directtly correlatable (ie say 1.6 from the former and something like 80% is 
cranked out by the later Vs 0.4 and 5% meaning no change)

Hope that helps, and if I am wrong about something somone corrects me.

Stephan Watkins

 Original-Nachricht 
> Datum: Thu, 20 Sep 2012 14:06:40 +0400
> Von: James Starlight 
> An: Discussion list for GROMACS users 
> Betreff: [gmx-users] Analysis of enssemble of MD trajectories

> Dear Gromacs Users!
> 
> 
> I'm working with the enssemble of the MD trajectories calculated for
> the common protein with the differences in the initial conditions in
> the case of each trajectory.
> 
> Now I'd like to perform analysis of that enssemble of data. For
> example I'de like to obtain RMSD as well as RMSF graphs calculated
> from all trajectories in one common graph for comparison of the
> dynamics of the systems.
> 
> I've used  trjcat on my 4 trajectories to obtain one merged trajectory
> multi.xtc and than tried to calculate RMSD for that multi.xtc but the
> resulted graph was wrong.
> 
> trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps
> -o multi.xtc
> 
> Is there any other way to do such analysis of several trajectories in
> common graph?
> 
> 
> James
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Re: [gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine

2012-09-18 Thread lloyd riggs

Dear All,

Ill give this a shot.  I guess it depends on your entire system (ie protein 
+DNA or just DNA) and what it is you waant to observe.

and example of why answereing becomes complex.  if A) I want to just look at 
say the total delta G,S or H.  I would only need to EQ several starting 
structures of the Thymine in conformation A, then several in conformation B. 
Then allow each to just run for a reasonable amount of time, in an NVT system. 
Then, you can just use the differences from the two to calculate the total 
energy change, but get no pretty curves, just simply a value.  This is 
relativly quick as it is essentially just long EQs.  I have done this, and it 
it fits biochem data from liturature.  But B) However, say you want the curves, 
or to compare positional or distance or other things (ionization, solvation), 
Then you have to take into account what you want to apply force on, ie a 
protein, the DNA as a whole or at varied positions along the bases, etc...and 
then follow the online tutorial for pull simulations.  If you are doing this 
and it is say just DNA, you then have to do dozens of runs, pulling along e
 ach base and holding the other fixed within reason,(like the complement, then 
the two on either direction or more...) most likely at several adjascent 
positions...to get a reflection of the real system.

Hope that helps in some way.  

Stephan Watkins

 Original-Nachricht 
> Datum: Tue, 18 Sep 2012 02:52:46 +
> Von: Christopher Neale 
> An: "gmx-users@gromacs.org" 
> Betreff: [gmx-users] Regarding Pulling simulation:To study the base flipping 
> of the thymine

> You can do this with the pull code. To do so, you need to define some sort
> of order parameter for which you have the base flipped in at one extreme
> and the base flipped out at the opposite extreme. There are lots of ways to
> do this and, unfortunately, there is no way to know what the best order
> parameter is without first evaluating it. Therefore, I suggest that you start
> with something simple like the distance between the NH of thymine and the
> NH of the paired guanine (assuming that you really have a TG pair). To pick
> the atom pair for the distance restraint, you can ideally look at a
> structure of equilibrium close association and find a pair of heavy atoms 
> that are
> close.
> 
> Chris.
> 
>  -- original message --
> 
> I am studying a system which consists of DNA duplex 20 base pairs.
> Actually
> I am interested in studying the base flipping of  the thymine.
> I have the crystal structure of extrahelical DNA  in which thymine is out
> side the helical structure. I want use pulling simulations to bring this
> base from extrahelical to Intrahelical  conformation, is there any way to
> do it in GROMACS pull code. Please see the figure below (link) for
> description.
> http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png
> 
> -- 
> Thanks and Regards,
> kartheek,
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Re: [gmx-users] Calculating number of water molecules involves between dimer protein.

2012-09-06 Thread lloyd riggs

Yeah,

I think based on some initial MDs I did with larger protein-protein interfaces 
there is an oscilatory aspect to most, like large bodies tied together with 
longerchains, where water moves in and out especially around edges, but 
woundered if it was protein specific or a global phenomina.  Just MDs without 
any pull forces, NPT equed for a while, then allowed to run for extensive 
periods of time.

Stephan Watkins

 Original-Nachricht 
> Datum: Thu, 06 Sep 2012 16:01:26 +1000
> Von: Mark Abraham 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Calculating number of water molecules involves 
> between   dimer protein.

> On 6/09/2012 3:56 PM, Rajiv Gandhi wrote:
> > I want to calculate the time dependence of the average number
> > of interfacial water molecules in dimer protein ( example hemoglobin),
> >
> > In experimental results proposed that the water molecules get
> > increase/decrease on time scale manner. Is't possible to show up this
> > process in MD simulation studies.
> 
> Sure. You just need to come up with a geometric definition for 
> interfacial and see what happens over a trajectory.
> 
> Mark
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Re: [gmx-users] Glycoproteion MD

2012-08-31 Thread lloyd riggs


Dear (sorry cant read chinese),

You can find some OPLS or 53a6 Parameters on the web by doing extensive 
searches, mostly they are free, but hosted on varied individual lab web sites.  
That, or it may be easier to define some sets of bonds (angles, dihedrials, 
lengths charges, etc...from either the CRC or national institute of standards) 
for a small subset of sugars, inclusive of the inter-chain bonds, and then just 
use the defined names you gave the sugar atoms (ie Cc for sugar carbon, Pc for 
phosphorylated to sugar, etc... as inclusive this would only be several to a 
dozen atom types or somthing)(then you can post it :-))...but it might be 
easier than trying to define things based on single sugar moieties available on 
the web, as you most likely would have errors when your suger moities are large 
from the inter-sugar bonds between subunits, such as a 10-20 length 
polysacharide on a glycosylated protein.  This is less trivial than it might 
seem, but would still take a few days, and you might be able to 
 use all but say 1-2 atoms if you find several defined parameters for sugars on 
the web already...

Sincerely,

Stephan Watkins

 Original-Nachricht 
> Datum: Fri, 31 Aug 2012 09:26:38 +0800
> Von: "陈应广" <525342...@qq.com>
> An: "gmx-users" 
> Betreff: [gmx-users] Glycoproteion  MD

> Dear all  I am interested in simulating a model of Glycoproteion. I
> could'nt find the define of the residue in any forcefield .rtp file of GMX. I 
> am
> using Gromacs 4.5.5 . If any one can help me in getting forcefield
> parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please
> suggest where else I should search for these.
>   
>  Thanking all
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Re: [gmx-users] Bins in wham analysis

2012-07-26 Thread lloyd riggs


True, I found the lower bin numbers makes the error change (increase), 
especially at ends of the run, howevere the mean values were the same.  I also 
checked with g_sham as comparision, and found again the means the same but 
differences in error (max and min values if I include all data).  So all three 
checks gave same mean, different (wider or lower) error (and I guess subsequent 
varience so is expected).

Interesting note, if I use sham, or wham, running wham on only a single 
trajectory, then merge them all by hand in a spread sheet (wham output), the 
wham has the same values as the sham?  Does anyone know why?

Stephan Watkins


 Original-Nachricht 
> Datum: Thu, 26 Jul 2012 06:46:04 -0400
> Von: Justin Lemkul 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Bins in wham analysis

> 
> 
> On 7/26/12 3:55 AM, neeru sharma wrote:
> > Dear Gromacs users,
> >
> > I have a query regarding the number of bins used in wham analysis.
> >
> > If I have performed by simulations over 15 umbrellas (15 different
> > staring structures), what should be the ideal number of bins to
> > perform wham analysis? Does it depend on the number of umbrellas. For
> > example:
> >
> > 1) Should I use more than 15 bins in my case, and the one that gives
> > proper overlap in histogram ?
> > 2) Or any number of bins (even if it is less than 12) can be used, if
> > I get proper overlap in my histogram output?
> >
> > Any suggestion is appreciated.
> >
> 
> The -bins option has to do with the final PMF profile.  The default value
> is 
> 200, and I would think that setting a low number like 12 or 15 would
> result in 
> very poor output.  I believe there is some discussion on this in the
> g_wham paper.
> 
> -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] How to speed up equilibrating the density of bulk system?

2012-07-17 Thread lloyd riggs

A variabvle thermostat that increases from 180 K to 300 K over cycles of 
100-1
 Original-Nachricht 
> Datum: Tue, 17 Jul 2012 20:40:12 +0800
> Von: Wu Chaofu 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] How to speed up equilibrating the density of bulk
> system?

> Dear gmxers,
> 
> I am trying to generate one polymer melt from one big enough box using
> NPT MD in gmx. I find that the density of system varies very slow.
> Could you please give me some hints about how to speed up this
> process? Thanks a lot for any reply.
> 
> Yours sincerely,
> 
> Chaofu Wu.
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Re: [gmx-users] Final state not reached in pulling simulation

2012-07-12 Thread lloyd riggs

your pull force looks insanly high especially if your pulling a small piece of 
residue?  But for a whole protein of averidge 40 KDa, or 350 amino acids its 
around 2000 to 3000 from liturature (only about 6 that I could find anyways).  
I might thus be wrong, but wounder if you have a pull rate and force what one 
wins?

Stephan

 Original-Nachricht 
> Datum: Thu, 12 Jul 2012 18:15:53 +0200
> Von: Thomas Schlesier 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] Final state not reached in pulling simulation

> It could be possible tht you do not pull into the 'right' direction. if 
> there is another group between 'GTP' and 'Residue' you will get clashes 
> and 'Residue' won't move further (could be a water molecule, or some 
> other part of 'GTP').
> If this happens you should observe an increase in the force due to the 
> umbrella potential.
> If the problems are due to waters molecules which block the 'pathway' 
> you could just delete them.
> If another group is in the way, you might want to change the pull-vector 
> (and if lucky find the right one). But don't know what would be the best 
> strategy in this case. Maybe you can look into what docking-people do, 
> seems to me that your simulation is related to what they do (but myself 
> has absolute no knowledge about docking simulations).
> 
> greetings
> thomas
> 
> 
> 
> Am 12.07.2012 17:26, schrieb gmx-users-requ...@gromacs.org:
> > Hello all,
> >
> > I m performing a pulling simulation on my Protein-Mg-GTP complex. I
> > have considered pulling between the GTP and a residue of protein.
> > The pull code in the .mdp file im using is as follows:
> >
> >
> > ; Pull code
> > pull= umbrella
> > pull_geometry   = distance  ; simple distance increase
> > pull_dim= N N Y
> > pull_start  = yes   ; define initial COM distance>  0
> > pull_ngroups= 1
> > pull_group0 = GTP
> > pull_group1 = Residue
> > pull_rate1  = -0.5  ; 0.5 nm per ps = .05 nm per ns
> > pull_k1 = 1  ; kJ mol^-1  nm^-2
> >
> >
> >
> > The initial distance between GTP and the residue was 7 A and the
> > desired one was 3A. After the completion of run (10ns), I could get a
> > trajectory where the final distance was still 4.25 A.
> >
> > I tried to continue the simulation for another 10ns with the same
> > value for pull_k1 parameter and one by increasing the value to 100,000
> > also. In both of the case, the  trajectories showed the distance
> > stabilized near _4.25 A only.
> > Can anyone please tell me the reason behind it? What should I do, so
> > that I could get the desired distance ?
> >
> > Any suggestion and help is welcome !!!
> >
> >
> > Thanks,
> >
> > Neeru Sharma
> 
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Re: [gmx-users] Re:Shell scripts

2012-07-06 Thread lloyd riggs

Thanks,

and thanks to Tsjerk.

Stephan

 Original-Nachricht 
> Datum: Fri, 06 Jul 2012 20:04:48 +1000
> Von: Mark Abraham 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:Shell scripts

> On 6/07/2012 6:27 PM, lloyd riggs wrote:
> > Yes,
> >
> > I was just going over them individually, then cat into a single spread
> sheet, which I can use awk to do combos, $1+$2+$16+$233...etc...
> 
> With Tsjerk's suggestion, and g_energy -xvg none, you can have such a 
> "spread sheet" from one .edr file written in one go.
> 
> Mark
> 
> >
> > Its still alot of files but easier to manipulate with complex .ndx files
> than just using g_energy every time...mostly time saving when you exceed
> 10 simulation or more.  Still, having to re-learn some basic awk, gawk, cat
> and piping skills from 12 years ago is a pain, but the simple things are
> invaluable with gromacs I would say.  Without them you would become so bogged
> one might hit insanity levels...
> >
> >
> > Thanks
> >
> > Stephan Watkins
> > University of Bern-Inselspital
> >
> >
> >  Original-Nachricht 
> >> Datum: Fri, 6 Jul 2012 07:09:16 +0200
> >> Von: Tsjerk Wassenaar 
> >> An: Discussion list for GROMACS users 
> >> Betreff: Re: [gmx-users] Re:Shell scripts
> >> Hey,
> >>
> >> I'd probably go for something like:
> >>
> >> for ((i=1; i<...; i++)); do echo $i 0 | g_energy ...; done
> >>
> >> Note the additional 0 to make g_energy exit. The (( )) has been in
> >> bash for ages, so that shouldn't be a problem.
> >>
> >> I notice that in the working construct you used 'traj_x.edr', while in
> >> the earlier ones, you used 'traj_${i}.edr'. If you try to extract all
> >> energy terms from a single .edr file, you can also use
> >>
> >> echo $(seq 1321) 0 | g_energy -f traj_x.edr -o stuff.xvg
> >>
> >> and then parse the columns out of the .xvg file.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >> On Fri, Jul 6, 2012 at 1:11 AM, Mark Abraham 
> >> wrote:
> >>> On 6/07/2012 7:25 AM, lloyd riggs wrote:
> >>>> Dear All,
> >>>>
> >>>> Thank you,
> >>>>
> >>>> I finally got this to work on the other PC after four hours...
> >>>>
> >>>> i=1
> >>>> while [ $i -le 1322 ]
> >>>> do
> >>>> g_energy -f traj_x.edr -o ${i}.xvg << EOF
> >>>> ${i}
> >>>>
> >>>> EOF
> >>>> i=$(($i+1))
> >>>> done
> >>>>
> >>>> Still can not figure out the difference, or why one works on one PC
> and
> >>>> not the other?
> >>>
> >>> Probably different bash versions, as your Ubuntu could well be more
> >> recent
> >>> than some version on a server at work. Try bash --version. If so, poke
> >> your
> >>> system admins to make an up-to-date bash available for you, even if
> not
> >> as
> >>> the system default.
> >>>
> >>> Mark
> >>>
> >>>
> >>>> Stephan (in Rainy Switzerland)
> >>>>
> >>>>  Original-Nachricht 
> >>>>> Datum: Thu, 5 Jul 2012 22:25:06 +0200
> >>>>> Von: Elton Carvalho 
> >>>>> An: Discussion list for GROMACS users 
> >>>>> Betreff: Re: [gmx-users] Re:Shell scripts
> >>>>> On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs 
> >> wrote:
> >>>>>> Does any one know why, or have some other scripts...
> >>>>>>
> >>>>> My suggestion would be something in the lines of
> >>>>>
> >>>>> #!/bin/bash
> >>>>>
> >>>>> for i in $(seq 2121) ; do
> >>>>> g_energy -f traj_${i}.edr -o ${i}.xvg <<< "${i} 0"
> >>>>> done
> >>>>>
> >>>>> ===
> >>>>>
> >>>>> Notice the "in" keyword right after 'i'.
> >>>>>
> >>>>> I used a subshell to invoke the program 'seq', which generates a
> >>>>> sequence from 1 to the given argument, so we don't depent om how
> these
> >>>>> other constructs with ((; ; )) work among

Re: [gmx-users] Re:Shell scripts

2012-07-06 Thread lloyd riggs

Yes,

One is a newer 12. version Vs. 11.10.  The one PC at home just ignores the for 
loop, and uses it as an infanite loop over everything while the other complains 
of syntax (vs.12).  The one "while" loop I posted works on both, and you can 
also catch averidges well by $> sh script.sh >> outterminaloutput.txt  If 
somone is interested in averidges.  For me they're not that important, except 
mayby solvent  wise.  I looked at it with terminal output and realized it went 
on for 10,000 or more steps/iterations over g_energy but didnt notice before is 
why it threw me off.

Thanks

Stephan Watkins
University of Bern-Inselspital

 Original-Nachricht 
> Datum: Fri, 06 Jul 2012 09:11:22 +1000
> Von: Mark Abraham 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:Shell scripts

> On 6/07/2012 7:25 AM, lloyd riggs wrote:
> > Dear All,
> >
> > Thank you,
> >
> > I finally got this to work on the other PC after four hours...
> >
> > i=1
> > while [ $i -le 1322 ]
> > do
> > g_energy -f traj_x.edr -o ${i}.xvg << EOF
> > ${i}
> >
> > EOF
> > i=$(($i+1))
> > done
> >
> > Still can not figure out the difference, or why one works on one PC and
> not the other?
> 
> Probably different bash versions, as your Ubuntu could well be more 
> recent than some version on a server at work. Try bash --version. If so, 
> poke your system admins to make an up-to-date bash available for you, 
> even if not as the system default.
> 
> Mark
> 
> >
> > Stephan (in Rainy Switzerland)
> >
> >  Original-Nachricht 
> >> Datum: Thu, 5 Jul 2012 22:25:06 +0200
> >> Von: Elton Carvalho 
> >> An: Discussion list for GROMACS users 
> >> Betreff: Re: [gmx-users] Re:Shell scripts
> >> On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs  wrote:
> >>> Does any one know why, or have some other scripts...
> >>>
> >>
> >> My suggestion would be something in the lines of
> >>
> >> #!/bin/bash
> >>
> >> for i in $(seq 2121) ; do
> >> g_energy -f traj_${i}.edr -o ${i}.xvg <<< "${i} 0"
> >> done
> >>
> >> ===
> >>
> >> Notice the "in" keyword right after 'i'.
> >>
> >> I used a subshell to invoke the program 'seq', which generates a
> >> sequence from 1 to the given argument, so we don't depent om how these
> >> other constructs with ((; ; )) work among different versions of bash.
> >>
> >> I also suggest replacing the here-document by a here-string, but
> >> that's personal taste. You may or may not have problems with older
> >> versions of bash
> >>
> >> Greetings from a foggy Groningen,
> >> -- 
> >> Elton Carvalho
> >> Tel.: +55 11 3091-6985/6922
> >> Dept Física dos Materiais e Mecânica
> >> Instituto de Física
> >> Universidade de São Paulo
> >> P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
> >> -- 
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Only plain text messages are allowed!
> >> * 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
> 
> 
> -- 
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Re: [gmx-users] Re:Shell scripts

2012-07-06 Thread lloyd riggs

Yes,

I was just going over them individually, then cat into a single spread sheet, 
which I can use awk to do combos, $1+$2+$16+$233...etc...

Its still alot of files but easier to manipulate with complex .ndx files than 
just using g_energy every time...mostly time saving when you exceed 10 
simulation or more.  Still, having to re-learn some basic awk, gawk, cat and 
piping skills from 12 years ago is a pain, but the simple things are invaluable 
with gromacs I would say.  Without them you would become so bogged one might 
hit insanity levels...


Thanks

Stephan Watkins
University of Bern-Inselspital


 Original-Nachricht 
> Datum: Fri, 6 Jul 2012 07:09:16 +0200
> Von: Tsjerk Wassenaar 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:Shell scripts

> Hey,
> 
> I'd probably go for something like:
> 
> for ((i=1; i<...; i++)); do echo $i 0 | g_energy ...; done
> 
> Note the additional 0 to make g_energy exit. The (( )) has been in
> bash for ages, so that shouldn't be a problem.
> 
> I notice that in the working construct you used 'traj_x.edr', while in
> the earlier ones, you used 'traj_${i}.edr'. If you try to extract all
> energy terms from a single .edr file, you can also use
> 
> echo $(seq 1321) 0 | g_energy -f traj_x.edr -o stuff.xvg
> 
> and then parse the columns out of the .xvg file.
> 
> Cheers,
> 
> Tsjerk
> On Fri, Jul 6, 2012 at 1:11 AM, Mark Abraham 
> wrote:
> > On 6/07/2012 7:25 AM, lloyd riggs wrote:
> >>
> >> Dear All,
> >>
> >> Thank you,
> >>
> >> I finally got this to work on the other PC after four hours...
> >>
> >> i=1
> >> while [ $i -le 1322 ]
> >> do
> >> g_energy -f traj_x.edr -o ${i}.xvg << EOF
> >> ${i}
> >>
> >> EOF
> >> i=$(($i+1))
> >> done
> >>
> >> Still can not figure out the difference, or why one works on one PC and
> >> not the other?
> >
> >
> > Probably different bash versions, as your Ubuntu could well be more
> recent
> > than some version on a server at work. Try bash --version. If so, poke
> your
> > system admins to make an up-to-date bash available for you, even if not
> as
> > the system default.
> >
> > Mark
> >
> >
> >>
> >> Stephan (in Rainy Switzerland)
> >>
> >>  Original-Nachricht 
> >>>
> >>> Datum: Thu, 5 Jul 2012 22:25:06 +0200
> >>> Von: Elton Carvalho 
> >>> An: Discussion list for GROMACS users 
> >>> Betreff: Re: [gmx-users] Re:Shell scripts
> >>> On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs 
> wrote:
> >>>>
> >>>> Does any one know why, or have some other scripts...
> >>>>
> >>>
> >>> My suggestion would be something in the lines of
> >>>
> >>> #!/bin/bash
> >>>
> >>> for i in $(seq 2121) ; do
> >>> g_energy -f traj_${i}.edr -o ${i}.xvg <<< "${i} 0"
> >>> done
> >>>
> >>> ===
> >>>
> >>> Notice the "in" keyword right after 'i'.
> >>>
> >>> I used a subshell to invoke the program 'seq', which generates a
> >>> sequence from 1 to the given argument, so we don't depent om how these
> >>> other constructs with ((; ; )) work among different versions of bash.
> >>>
> >>> I also suggest replacing the here-document by a here-string, but
> >>> that's personal taste. You may or may not have problems with older
> >>> versions of bash
> >>>
> >>> Greetings from a foggy Groningen,
> >>> --
> >>> Elton Carvalho
> >>> Tel.: +55 11 3091-6985/6922
> >>> Dept Física dos Materiais e Mecânica
> >>> Instituto de Física
> >>> Universidade de São Paulo
> >>> P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Only plain text messages are allowed!
> >>> * 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
> &g

Re: [gmx-users] Re:Shell scripts

2012-07-05 Thread lloyd riggs

Dear All,

Thank you,

I finally got this to work on the other PC after four hours...

i=1
while [ $i -le 1322 ] 
do
g_energy -f traj_x.edr -o ${i}.xvg << EOF
${i}

EOF
i=$(($i+1))
done

Still can not figure out the difference, or why one works on one PC and not the 
other? 

Stephan (in Rainy Switzerland)

 Original-Nachricht 
> Datum: Thu, 5 Jul 2012 22:25:06 +0200
> Von: Elton Carvalho 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:Shell scripts

> On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs  wrote:
> >
> > Does any one know why, or have some other scripts...
> >
> 
> 
> My suggestion would be something in the lines of
> 
> #!/bin/bash
> 
> for i in $(seq 2121) ; do
> g_energy -f traj_${i}.edr -o ${i}.xvg <<< "${i} 0"
> done
> 
> ===
> 
> Notice the "in" keyword right after 'i'.
> 
> I used a subshell to invoke the program 'seq', which generates a
> sequence from 1 to the given argument, so we don't depent om how these
> other constructs with ((; ; )) work among different versions of bash.
> 
> I also suggest replacing the here-document by a here-string, but
> that's personal taste. You may or may not have problems with older
> versions of bash
> 
> Greetings from a foggy Groningen,
> -- 
> Elton Carvalho
> Tel.: +55 11 3091-6985/6922
> Dept Física dos Materiais e Mecânica
> Instituto de Física
> Universidade de São Paulo
> P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
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[gmx-users] Re:Shell scripts

2012-07-05 Thread lloyd riggs


Dear All,

So I am using some scripts to parse through 100s of files using bash and awk.  
In any case, I run into a problem as follows;  I have Ubuntu at home on my PC 
and I have a laptop at work with Ubuntu, same versions libraries, everything.  
When I run the scripts at home they work fine, when I run them at the Ubuntu at 
work I get errors ranging from "Bad for loop variable" all the way to an 
infanite done at end of line no matter how much you type done.

Does any one know why, or have some other scripts...

Examples of just parsin energy files:

#!/bin/bash
i=1
for ((i=1;i<=1322;i+=1)); do
g_energy -f traj_${i}.edr -o ${i}.xvg << EOF
${i}
EOF
done

or infanite loops

#!/bin/bash
i=1
for (( ; ;)); do
g_energy -f traj_${i}.edr -o ${i}.xvg << EOF
${i}
EOF
done

or range

#!/bin/bash

for i {1..2121} ; do
g_energy -f traj_${i}.edr -o ${i}.xvg << EOF
${i}
EOF
i=$(($i+1))
done

or while loop

#!/bin/bash
i=1while [ i -le 2121 ]; do
g_energy -f traj_${i}.edr -o ${i}.xvg << EOF
${i}
EOF
done

Ill forgo the awk or cat extensions,

does anyone know why? Or have some other pasing scripts they've jimmied?

Stephan
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Re: [gmx-users] Modifying Lennard-Jones cross term

2012-07-04 Thread lloyd riggs

Well,

Ill give that a shot from memory of a discussion some time ago, which you could 
probably track down on the e-mails of past search engine.  I think it has to do 
with force field types, either they list the sigma values, or direct 6, 12 or 
derived LJ parameters,  so it would be related to which force field you use.

Otherwise they are in the .rtp, .itp files for specific force fields as tables, 
and I assume as such you could then put anything you wished in there real or 
not, as the software would just take the table value.

Although I assume someone else has more direct advice, personally though I dont 
think there would be much of a difference of it unless your atoms pairs have 
different sigma values than those used in gromacs.  You might, if you wished 
only 2 atoms, have to define an entry for those explicitly, giving some names 
different from the other things in the .rtp, .itp files, then the respective 
sigmas in the parameters.  The bulletin/email list also has ample things on 
this (modification of the files) as well, but the files are all strait forward 
if you just look at them in an editor.  Defining the resultant, (example 
sigma_12) might be hard however, as in either case it still plugs in the 
parameter to an equation.

Otherwise you could plot distances and do the lj calculation by hand, but it 
might get heck-tick if you include any solvent, or other effects...

Good luck

Stephan Watkins

 Original-Nachricht 
> Datum: Wed, 4 Jul 2012 17:45:56 +0900 (KST)
> Von: Hyungjun Kim 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] Modifying Lennard-Jones cross term

>Dear GMX users,
> 
>This is Hyungjun Kim.
> 
>I try to modify the len?ard jones parameter explicitly.
> 
>I knew that gromacs provide the com?ination rule such as
>sigma_12=(sigma_1 + sigma_2 ) /2 like.
> 
>I fin? that some specific interaction is quite important, so I want to
>give expl?cit sigma_12 value for some combination.
> 
>Could you give me any advi?e?
> 
>Thank you in advance.
> 
>Regards,
> 
>김형??D8 드림
> 
>---
>Hyungjun Kim,
>Quantum and Computation?l Chemistry Laboratory,
>Department of Chemistry, KAIST,
>Daejeon 305?701, Korea
>e-mail: [1]hyungjun96?kaist.ac.kr or [2]jun0906@kai?t.ac.kr
> 
>phone : 042-350-2861
> 
>mobile phone : 010-8537-5051
> 
>web : http://qclab.kaist.ac.kr
> 
> References
> 
>Visible links
>1. file:///tmp/3D"mailto:hyungju...@kaist.ac.kr";
>2. file:///tmp/3D"mailto:jun0...@kaist.ac.kr";
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Re: [gmx-users] Regarding umbrella sampling simulations along H-bonds

2012-06-29 Thread lloyd riggs

Dear Neeru Sharma,

I know off hand from years of work with Mg-GTP sites, they are realativly 
rigid/staritforward.  If the bonds arn't present with occupied GTP, or Mg at 
the beggining, you should equilabrate your starting structures more.  Unless 
your looking at the GTP binding to Mg in which case, the Mg bonds should at 
least be present.  Mg wont leave the site under norm conditions, unless the 
protein is unfolded (or recycled in cell biological or biochemical terms), or 
outcompeted with a higher affine ion.

> Can anyone suggest me what parameters or pull_geometry shall I use, to
> perform the same. Any suggestion is welcome!

Thats too experiment specific to say, without knowing what your trying to look 
at.

Grüess

Stephan Watkins

 Original-Nachricht 
> Datum: Thu, 28 Jun 2012 23:30:38 +0530
> Von: neeru sharma 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] Regarding umbrella sampling simulations along H-bonds

> Dear Gromacs Users,
> 
> I am simulating a system containing Protein-Mg-GTP complex.
> 
> I intend to perform the umbrella sampling on the system to calculate
> PMF and to perform wham analysis.
> I have generated a series of conformations for the umbrella sampling.
> My main consideration is towards the 2 H-bonds: one between Protein
> and MG and other one between protein and GTP. Both of these bonds were
> absent during the start of the simulation but formed when the
> simulation was completed.
> 
> Can anyone suggest me what parameters or pull_geometry shall I use, to
> perform the same. Any suggestion is welcome!
> 
> 
> --
> Thanks and regards,
> Neeru
> -- 
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Re: [gmx-users] Free energy between residues

2012-06-28 Thread lloyd riggs

>>> I work in UK, London. Why are you asking?

Because Im a super cop.  No I just woundered about people with gmail, yahoo, or 
like mine gmx as to where they are at, etc...

Ive been doing something similar, and it fits with whats expected, however what 
Justin said is true, without knowing what your doing, or how inclusivly your 
doing it, it may or may not make sense.  In my case I may either be lucky, or 
something of the sort...

That, and I was trying to post a little, as I read the post extensivly and find 
them helpfull sometimes...but post little other than a lame thing here and 
there.  

Stephan Watkins
University of Bern,
Department of Allergy, rheumatology and immunology
Bern 3011
Switzerland
0041 31 632 43 22/42 33

 Original-Nachricht 
> Datum: Thu, 28 Jun 2012 07:19:14 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Free energy between residues

> 
> 
> On 6/28/12 6:51 AM, Steven Neumann wrote:
> > On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul 
> wrote:
> >>
> >>
> >> On 6/28/12 6:33 AM, Steven Neumann wrote:
> >>>
> >>> On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs 
> wrote:
> >>>>
> >>>> Dear Steven,
> >>>>
> >>>> Where are you working?
> >>>
> >>>
> >>> I work in UK, London. Why are you asking?
> >>>
> >>>
> >>>> >From my experience the g_energy  -fee only gives a free enrgy
> estimate
> >>>> for the whole system, so one has to pull out all the energy terms
> based on
> >>>> your index file of interest and sum them in a spread sheet.  if the
> -fee can
> >>>> do the energy estimates for a specific set, please let me know this
> would be
> >>>> valuable to me.
> >>>
> >>>
> >>> I think I will just need a potential energy between those residues (LR
> >>> and Coulombic) and then can get the effective potential
> >>> Ueff=-kTln >>> and then g_dist.
> >>>
> >>
> >> If you are using PME, there is no trivial way to decompose the
> reciprocal
> >> space term.
> >>
> >> -Justin
> >
> > But if I will get the effective potential with respect to the distance
> > I can adjust non bonded parameters to this curve in coarse grained
> > model. Am I right?
> >
> 
> Honestly, I have no idea on what intend to adjust.  Certainly you can
> tweak 
> things in any way you like, but that doesn't mean the answer makes sense
> or that 
> what you've done is justifiable.  To me, umbrella sampling seems far more 
> 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] Free energy between residues

2012-06-28 Thread lloyd riggs

Dear Steven,

Where are you working?

>From my experience the g_energy  -fee only gives a free enrgy estimate for the 
>whole system, so one has to pull out all the energy terms based on your index 
>file of interest and sum them in a spread sheet.  if the -fee can do the 
>energy estimates for a specific set, please let me know this would be valuable 
>to me.

Sincerely,

Stephan Watkins

 Original-Nachricht 
> Datum: Thu, 28 Jun 2012 09:28:09 +0100
> Von: Steven Neumann 
> An: Discussion list for GROMACS users 
> Betreff: [gmx-users] Free energy between residues

> Dear Gmx Users,
> 
> I want to obtain the free energy difference between the pair of
> residues in my protein chain with respect to thheir distance. Would
> combinbation:
> 
> 1) g_dist - distances between two groups during the simulation time
> 
> 2) g_energy -fee (DelatG - with energy groups I am interested in
> stated in mdp file)
> 
> give me those values?
> 
> Or I should use PMF - umbrella sampling with the bias (harmonic)
> potential introduced?
> 
> Thank you,
> 
> Steven
> -- 
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Re: [gmx-users] wrong distances with g_dist

2012-06-27 Thread lloyd riggs

Dear Dmytro Kovalskyy,

The ARG CZ is at the end (tip of the ARG), what does the distances look like 
over time?  A floppy long amino acid?  And your actual distance calculation?  
Is it from a graphics/pdb file, or how is it measured?

Stephan

 Original-Nachricht 
> Datum: Tue, 26 Jun 2012 16:14:31 -0500
> Von: Dmytro Kovalskyy 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] wrong distances with g_dist

> Hi,
> 
> I try to calculate distance between two atoms with g_dist. Somewhat I get 
> distance lower than actual.
> Here there are coordinates of the two atoms (PDB format)
>  
> ATOM702  CZ  ARG X  45   5.930   9.230  41.740  0.00  0.00
> ATOM   2751  CA  PHE X 177  41.710  45.000  27.180  0.00  0.00
> 
> And the distance I get from g_dist is 4.6260725 nm while the actual is
> 5.265 
> nm.
> 
> What the problem can be?
> 
> Dmytro
> 
> 
> 
> 
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Re: [gmx-users] Re: umbrella sampling with distances larger than half box size

2012-06-25 Thread lloyd riggs

Thanks,

You should make sure your WHAM is good, or your DNA isnt moving out of the box, 
as I watched a series of questions reply here before which showed that 
irrelevant WHAM data might be produced when the molecule leaves the box edges, 
ie you would be missing a piece or have a negative where the positive number 
should be in the calculations used inside WHAM.

Grüess

Stephan

 Original-Nachricht 
> Datum: Mon, 25 Jun 2012 02:32:40 -0700 (PDT)
> Von: anaome 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] Re: umbrella sampling with distances larger than half
> box size

> Thanks Stephan for your suggestions,
> 
> A finally found a solution for distance larger than half the box size:
> 1) Regenerate the tpr files with pbc=no
> 2) Perform WHAM analysis with the umbrella forces (-if)
> 
> 
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/umbrella-sampling-with-distances-larger-than-half-box-size-tp4998779p4998782.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> -- 
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Re: [gmx-users] umbrella sampling with distances larger than half box size

2012-06-24 Thread lloyd riggs

I would wait for others to answere but,

a) you might try orienting your circular DNA in a visual program first and then 
use say just pull nny or something just as it makes it easier to see output and 
makes restraints nicer in output,

b) the pull k1 might be larger for an effect on macromolecules, ie in some 
protein work its around 2000-3000 but I have also seen some with 1000, however 
these are 300-1000 aminos or larger proteins so do not know how it would 
translate to DNA

c) Just increase your deminsions in 1 direction from the pull defined in a) or 
your origional vector

Aside,  Like I said Im a novice so others might have more usefull information.

Stephan Watkins

 Original-Nachricht 
> Datum: Sun, 24 Jun 2012 13:09:34 +0200
> Von: ana...@fundp.ac.be
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] umbrella sampling with distances larger than half box
> size

> Dear Users,
> 
> I am performing umbrella sampling simulations of the ring closure of  
> DNA minicircles. The problem with pull_geometry=distance is that the  
> end-to-end distance used as general coordinate becomes at some point  
> larger than half the box size. The distance to the closest image is  
> used in the histogram generation and WHAM procedure what is of course  
> wrong. To avoid this problem I tried pull_geometry=direction_periodic  
> with pull_vec1 taken as the vector between both ends of the DNA  
> fragment and one end frozen but this set-up does not seem to work  
> properly. Does anyone have a solution? Is there a possibility to  
> implement a pull_geometry=distance_periodic in a next version of  
> gromacs?
> 
> Thank you for helping!
> 
> Below are the relevant options used for umbrella sampling:
> pull = umbrella
> pull_geometry= distance
> pull_dim = Y Y Y
> pull_start   = yes
> pull_ngroups = 1
> pull_group0  = start
> pull_group1  = end
> pull_k1  = 100
> 
> 
> pull = umbrella
> pull_geometry= direction_periodic
> pull_dim = Y Y Y
> pull_start   = yes
> pull_ngroups = 1
> pull_group0  = start
> pull_group1  = end
> pull_vec1=-0.4160005.3 -0.2650005.3 -2.4920005.3
> pull_k1  = 100
> freezegrps   = start
> freezedim= Y Y Y
> 
> 
> 
> -- 
> Aymeric Naômé
> Ph. D. Student
> UCPTS Division
> University of Namur
> 61 Rue de Bruxelles
> 5000 Namur
> BELGIUM
> 
> 
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Re: [gmx-users] About Mike Harms python script

2012-06-17 Thread lloyd riggs

Dear Vidhyh Sankar,

>IndexError: list index out of range

When a program reads in lists or arrays, in the software there is usually a set 
size, for lines or number of atoms, etc... If the array or list is longer than 
the set value you get this error.  Also, if a counter is off, ie stops one 
short through an iteration usually from not reading lines properly or geting a 
returned length for an index which has changed in length...

It either means one of the following:

2 of your files dont match in size (ie number of atoms)
1 of your files has the formatting wrong, ie lines are speced too long, so it 
doesnt read them properly
or theres a problem with the script, where it gets incorrect index lenghts.

if you look at the lines mentioned in the setupUmbrella.py script, it will tell 
you exactly what it is trying to read in, and you can then either know if its 
missmatch, or your files are formatted wrong.

Id wait and see, somone might be able to tell you off the bat exactly what the 
error is though.  In my experience, it can often be a secound carriage return 
or space at the end of a .gro, or .dat or .sh file.

Stephan Watkins

 Original-Nachricht 
> Datum: Sat, 16 Jun 2012 23:49:06 +0800 (SGT)
> Von: vidhya sankar 
> An: "gmx-users@gromacs.org" 
> Betreff: [gmx-users] About Mike Harms python script

> Dear justin  Thank you for your previous reply
> 
>   I am doing  Umbrella sampling in
> gromacs 
> 
> I have 30 set of initial configuration in .gro file format .Now i would
> like to do NPT equilibration and  umbrella sampling for all these
> configuration  (for these i have to carry out 30 times equilibration and 30 
> times
> umbrella sampling)  to  Automate these process i used the python script
> provided by Mike Harms. but when invoke the command as follows
> ./setupUmbrella.py summary_distances.dat 0.2 run-umbrella.sh &>
> caught-output.txt
> I got error as follows in Caught_output .txt
> 
> 
> Traceback (most recent call last):
>   File "./setupUmbrella.py", line 182, in 
>     out = main() 
>   File "./setupUmbrella.py", line 150, in main
>     distance_table = readDistanceFile(distance_file)
>   File "./setupUmbrella.py", line 49, in readDistanceFile
>     value = float(columns[1])
> IndexError: list index out of range
> 
> I  have all the required files ( index.ndx files , dist.xvg files, , .gro
> files and .mdp files) in the  running directory
> 
> How to solve these error
> Thanks In advance

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Re: [gmx-users] GPU crashes

2012-06-07 Thread lloyd riggs

Did you play with the time step?  Just currious, but I woundered what happened 
with 0.0008, 0.0005, 0.0002.  I found if I had a good behaving protein, as soon 
as I added a small (non-protein) molecule which rotated wildly while attached 
to the protein, it would crash unless I reduced the time step to the above when 
constraints were removed after EQ ... always it seemed to me it didnt like the 
rotation or bond angles, seeing them as a violation but acted like it was an 
amino acid? (the same bond type but with wider rotation as one end wasnt fixed 
to a chain)  If your loop moves via backbone, the calculated angles, bonds or 
whatever might appear to the computer to be violating the parameter settings 
for problems, errors, etc as it cant track them fast enough over the time step. 
Ie atom 1-2-3 and then delta 1-2-3 with xyz parameters, but then the particular 
set has additional rotation, etc and may include the chain atoms which bend 
wildly (n-Ca-Cb-Cg maybe a dihedral) but probab
 ly not this. 

Just a thought but probably not the right answere as well, it might be the way 
it is broken down (above) over GPUs, which convert everything to matricies 
(non-standard just for basic math operations not real matricies per say) for 
exicution and then some library problem which would not account for long range 
rapid (0.0005) movements at the chain (Ca,N,O to something else) and then tries 
to apply these to Cb-Cg-O-H, etc using the initial points while looking at the 
parameters for say a single amino acid...Maybe the constraints would cause 
this, which would make it a pain to EQ, but this allowed me to increase the 
time step, but would ruin the experiment I had worked on as I needed it 
unconstrained to show it didnt float away when proteins were pulled, etc...I 
was using a different integrator though...just normal MD.  

ANd your cutoffs for vdw, etc...Why are they 0?  I dont know if this means a 
defautl set is then used...but if not ?  Wouldnt they try integrating using 
both types of formula, or would it be just using coulumb or vice versa? (dont 
know what that would do to the code but assume it means no vdw, and all coulumb 
but then zeros are alwyas a problem for computers).  

Thats my thoughts on that.  Probably something else though.

Good luck,

Stephan

 Original-Nachricht 
> Datum: Wed, 06 Jun 2012 18:42:45 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: [gmx-users] GPU crashes

> 
> Hi All,
> 
> I'm wondering if anyone has experienced what I'm seeing with Gromacs 4.5.5
> on 
> GPU.  It seems that certain systems fail inexplicably.  The system I am
> working 
> with is a heterodimeric protein complex bound to DNA.  After about 1 ns of
> simulation time using mdrun-gpu, all the energies become NaN.  The
> simulations 
> don't stop, they just carry on merrily producing nonsense.  I would love
> to see 
> some action regarding http://redmine.gromacs.org/issues/941 for this
> reason ;)
> 
> I ran simulations of each of the components of the system individually -
> each 
> protein alone, and DNA - to try to track down what might be causing this 
> problem.  The DNA simulation is perfectly stable out to 10 ns, but each
> protein 
> fails within 2 ns.  Each protein has two domains with a flexible linker,
> and it 
> seems that as soon as the linker flexes a bit, the simulations go poof. 
> Well-behaved proteins like lysozyme and DHFR (from the benchmark set) seem
> fine, 
> but anything that twitches even a small amount fails.  This is very
> unfortunate 
> for us, as we are hoping to see domain motions on a feasible time scale
> using 
> implicit solvent on GPU hardware.
> 
> Has anyone seen anything like this?  Our Gromacs implementation is being
> run on 
> an x86_64 Linux system with Tesla S2050 GPU cards.  The CUDA version is
> 3.1 and 
> Gromacs is linked against OpenMM-2.0.  An .mdp file is appended below.  I
> have 
> also tested finite values for cutoffs, but the results were worse
> (failures 
> occurred more quickly).
> 
> I have not been able to use the latest git version of Gromacs to test
> whether 
> anything has been fixed, but will post separately to gmx-developers
> regarding 
> the reasons for that soon.
> 
> -Justin
> 
> === md.mdp ===
> 
> title   = Implicit solvent test
> ; Run parameters
> integrator  = sd
> dt  = 0.002
> nsteps  = 500   ; 1 ps (10 ns)
> nstcomm = 1
> comm_mode   = angular   ; non-periodic system
> ; Output parameters
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstxtcout   = 1000  ; every 2 ps
> nstlog  = 5000  ; every 10 ps
> nstenergy   = 1000  ; every 2 ps
> ; Bond parameters
> constraint_algorithm= lincs
> constraints = all-bonds
> continuation= no; starting up
> ; required cutoffs for implicit
> nstlist = 0
> ns_type = grid
> rlist   = 0

Re: [gmx-users] Trajectories

2012-06-05 Thread lloyd riggs


 Original-Nachricht 
> Datum: Tue, 05 Jun 2012 09:05:09 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Trajectories

> 
> 
> On 6/5/12 9:02 AM, rankinb wrote:
> > I am interested in pulling out the trajectories (x,y,z coordinates) of
> water
> > molecules within a certain distance of my solute molecule.  I have tried
> > using g_select, but that will only give me the atom numbers and not the
> > trajectories.  I can create an index file using this command but
> > unfortunately each time frame is set as a different group.
> >
> > Is there a way to get the trajectories at all frames of only the water
> > molecules within a specified distance of a solute molecule?
> >
> 
> At present, there is no elegant way to construct such a trajectory, since,
> in 
> principle, each frame can have a different number of atoms based on which
> water 
> molecules satisfy the given criteria.  Each index group that g_select
> provides 
> corresponds to an individual frame in the original trajectory, which you
> can use 
> to pull out individual coordinate files.  Perhaps a multi-frame .pdb or
> .gro 
> file would work, but I believe that .xtc and .trr files have to have the
> same 
> number of atoms in each frame to be interpreted correctly.
> 
> -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] Trajectories

2012-06-05 Thread lloyd riggs

Dear Rankinib,

You can do it with a 5 line bash script as well, cat everything times x,y,z and 
just cut and past them into a spread sheet, and save it with tabs or spaces.

Stephan Watkins

 Original-Nachricht 
> Datum: Tue, 05 Jun 2012 09:05:09 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Trajectories

> 
> 
> On 6/5/12 9:02 AM, rankinb wrote:
> > I am interested in pulling out the trajectories (x,y,z coordinates) of
> water
> > molecules within a certain distance of my solute molecule.  I have tried
> > using g_select, but that will only give me the atom numbers and not the
> > trajectories.  I can create an index file using this command but
> > unfortunately each time frame is set as a different group.
> >
> > Is there a way to get the trajectories at all frames of only the water
> > molecules within a specified distance of a solute molecule?
> >
> 
> At present, there is no elegant way to construct such a trajectory, since,
> in 
> principle, each frame can have a different number of atoms based on which
> water 
> molecules satisfy the given criteria.  Each index group that g_select
> provides 
> corresponds to an individual frame in the original trajectory, which you
> can use 
> to pull out individual coordinate files.  Perhaps a multi-frame .pdb or
> .gro 
> file would work, but I believe that .xtc and .trr files have to have the
> same 
> number of atoms in each frame to be interpreted correctly.
> 
> -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] How GROMACS calculate the energy of hydrogen bond

2012-05-31 Thread lloyd riggs

Dear All,

I have no clue what specifically you are trying, but I feal bad for all the 
physicist and quantum chemist whom have provided the software and continued to 
develop it.

Scanning in my free time, it seems a large amount of confusion on what people 
are trying to do stems from differences in what is taught textbook wise for 
things.

For instance a hydrogen bond to a physicist is an integration over space in 3 
dimensions including time and probabilities of occupied spaces (atom position 
variabilities reflected even more in proteins, ie the necessity of multiple MD 
runs with different starting conformations), Vs.  an organic chemist whom has 
cut offs, ie angles between two points and set distances between two atoms 
which generally reflect the means of calculated chemical energies within a 
range (say 80-90% which represent means, but usually from raw small molecules 
as determinants), Vs. Biologist whom have tables which either use a set 
distance and angle and little account of variability over time (ie a hydrogen 
bond equals 1.4 kCal/mol reflecting the absolute mean), conformations in amino 
acids, etc...

I think with gromacs it is very precise, as even the smallest energies between 
two interacting atoms is taken into account with accuracy reflected by the 
force fields used, and how they were derived.

Good luck, your going to start seeing more and more a flood of biologist.

Stephan Watkins

 Original-Nachricht 
> Datum: Thu, 31 May 2012 19:54:04 +1000
> Von: Mark Abraham 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond

> On 31/05/2012 7:46 PM, Acoot Brett wrote:
> > Hi Mark,
> >
> > It is confusing. As you know, for the same hydrogen bond in a protein, 
> > the related hydrogen bond angle and bond length can vary within a 
> > scope during the whole simulation process, however this small 
> > vibration of the hydrogen bond angle and length can lead to 
> > significant energy change, and correspondingly the energy of a 
> > hydrogen bond in simulation can be varied significantly. In comparison 
> > with hydrophobic effect, it would be too much is the energy of the 
> > hydrogen bond would be  not calculated  continuously.
> 
> It isn't, if the model physics isn't paramtrized to include it 
> explicitly - which is the case for all the force fields in GROMACS.
> 
> >
> > Could you give some further clarification?
> 
> What are trying to do? Measuring "the strength of a hydrogen bond" 
> requires you identify a state with and without it and a path between 
> them over which you can integrate.
> 
> Mark
> 
> >
> > Cheers,
> >
> > Acoot
> >
> > 
> > *From:* Mark Abraham 
> > *To:* Discussion list for GROMACS users 
> > *Sent:* Thursday, 31 May 2012 4:48 PM
> > *Subject:* Re: [gmx-users] How GROMACS calculate the energy of 
> > hydrogen bond
> >
> > On 31/05/2012 4:42 PM, Acoot Brett wrote:
> >> Dear All,
> >> The value of the energy of the hydrogen bond has relation with 
> >> distance and angle of the hydrogen bond related atoms. As for in the 
> >> simulation process, the distance and angle of the hydrogen bond 
> >> related atoms may change continuously. Will you please let me know 
> >> based on which formula GROMACS calculated the value of the energy of 
> >> the hydrogen bonds?
> >
> > There is no such formula used in MD force fields implemented in 
> > GROMACS. The only non-bonded interactions are the ones you already 
> > know about: electrostatics and VDW.
> > Observables like hydrogen bonds and the hydrophobic effect arise from 
> > them.
> >
> > Mark
> >
> > -- 
> > gmx-users mailing list gmx-users@gromacs.org 
> > 
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Re: [gmx-users] crude interaction energy using g_energy

2012-05-28 Thread lloyd riggs

I think the reality of biological systems is represented as such accurately.  
Everyone always strives in biochemistry for a precise number, ie binding 
affinity = 489.489 exactly.  In real systems there are to many variables 
(solvent, ions, particular position of moving amino acids at point A or B, 
etc...).  The original rule of thumb for beginning to study these systems was 
to do >100 MD simulations, but I personally think a small sample space will 
give you the same exact mean and STD deviation, STD error, etc... (ie 10-20 
runs).  There is, as larger MD's are now becoming more common still no set 
standard for this.

A quick way, which also generates the same variability but is faster (if you 
dont want a nice curve and just the end mean value) is to do MD A at the bound 
position and EQ it for a couple nano seconds using NV P and T, and then state B 
unbound the same, then 20 runs is manageable time wise, but you get no pretty 
curves, ie no transition states which are of interest in many cases, such as 
particular amino acids, or conformational changes which include several states.

I think this might help, although some analysis tools for large scale 
biological systems (ie say pulling contributions energy wise for a particular 
amino acid) would be an asset...as I have found none that dont require pulling 
energies, etc...alot of work at the moment.

Stephan Watkins
Univerity of Bern

 Original-Nachricht 
> Datum: Sun, 27 May 2012 20:44:48 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] crude interaction energy using g_energy

> 
> 
> On 5/27/12 8:41 PM, sai nitin wrote:
> > Dear all,
> >
> > Recently i performed  two 15ns simulation of  protein-ligand systems
> using
> > gromacs of my interest...and using g_energy tool..i calculated crude
> > interaction energy based on short-‐range energy components Eint =
>  +
> > . ...I got two Eints for two simulations
> >
> > 1) Eint = -51.003 Kcal/mol (first simulation)
> > 2) Eint = -26.615 Kcal/mol (second simulation)
> >
> > Can anybody tell me what meaning can i make out of it...means is first
> > simulation is more stable than second one..or vice versa...
> >
> 
> I don't think you can say anything about stability based on these figures.
>  In 
> simulation 1, the interaction is more stable than in simulation 2.  It
> seems 
> clear that the two simulations behaved somewhat differently, but the exact
> differences will only become apparent through other analyses and
> visualization.
> 
> -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] Wierd results from Umbrella sampling

2012-05-16 Thread lloyd riggs

One thought from justins post in the past,

Look at the .trj in VMD with the unit cell box and see if something sticks out 
at the end (ie comes up in the bootmn of the box from the top).  It then does 
what you show, however it may not be that.  If it is, you'll have to increase 
your box deminsion in the pull dir. and re-run it or throw out the data after 
it turns negative...

Steve

 Original-Nachricht 
> Datum: Wed, 16 May 2012 10:08:06 +0200
> Von: "Du Jiangfeng (BIOCH)" 
> An: "gmx-users@gromacs.org" 
> Betreff: [gmx-users] Wierd results from Umbrella sampling

> Dear Sir/Madam,
> 
> I have performed umbrella pulling and umbrella sampling my protein from a
> DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
> suddenly turns to zero at the last 1 nm) and the histograph does not show
> any overlap. Actually, I did it strictly based on Justin's tutorial, with
> the sample spacing of 0.2 nm.
> 
> Here are some lines from the end of the energy file (The energy should not
> decrease since it was in summation):
> 
> Distance(nm)  Energy (Kcal/mol)
> 5.288348  5.705318e+01
> 5.316250  4.881724e+01
> 5.344152  4.022505e+01
> 5.372054  3.101854e+01
> 5.399956  2.208200e+01
> 5.427858  1.343340e+01
> 5.455761  4.267619e+00
> 5.483663  -5.084078e+00  ? minus
> 5.511565  -1.486168e+01  ? minus
> 5.539467  -2.393515e+01  ? minus
> 5.567369  -3.343453e+01  ? minus
> 
> 
> Followings are some lines from the end of histograph file:
> 
> Distance(nm)
> 5.455761  0   0   0   0   0   0   0   0   
> 0   0   0   0   0   0   0   0   0   0 
>   8   
> 5.483663  0   0   0   0   0   0   0   0   
> 0   0   0   0   0   0   0   0   0   0 
>   8   
> 5.511565  0   0   0   0   0   0   0   0   
> 0   0   0   0   0   0   0   0   0   0 
>   12  
> 5.539467  0   0   0   0   0   0   0   0   
> 0   0   0   0   0   0   0   0   0   0 
>   4   
> 5.567369  0   0   0   0   0   0   0   0   
> 0   0   0   0   0   0   0   0   0   0 
>   2   
> 
> 
> I am really depressed because it took me quiet a long time to sampling but
> it seems in vain... I really no idea to find out what went wrong. 
> 
> I am looking forward to your help. Thanks a lot.
> 
> Jiangfeng.
> 
>   
> 
> 
> Jiangfeng Du, PhD Student
> Cardiovascular Research Institute Maastricht
> Department of Biochemistry
> P.O. Box 616
> Mobile: +31-681741859
> FAX: +31-43-3884159
> 6200 MD Maastricht
> The Netherlands-- 
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Re: [gmx-users] Re: Data Analysis

2012-04-20 Thread lloyd riggs


> 
> This sounds to me like a periodicity issue.  Were these runs conducted
> with 
> "pull_geometry = distance"?  If so, were the COM distances always less
> than half 
> of the box vector along the restrained dimension(s)?  Are you running with
> NPT? 
>   If the answer to any or all of these is "yes," then you could have a
> problem 
> with the pull algorithm failing due to periodicity.  The sign changes
> might 
> account for that.  You wouldn't see any weird periodic jumps, but the size
> of 
> the box and the COM distance at the instance of the sign/magnitude change
> would 
> coincide.
> 

Merci,

As the swiss say.  At the very end one or two amino acids look out of the box 
into the botomn again in 1 run especially.

>A mean is only as good as the error associated with it.  No error >estimate, 
>no confidence in the value.

Well I trust the results except one or two points.  The means stay the same 
between the mentioned points, but the STDDEV and STD error double, as it is 
2000 points or so, it just looks like a smooth curve with a linear (really 
leanear) spike.  I dont thinks its that big an issue though comparativly, as 
one does not loose the overall curve reguardless.

Thanks for your advice, suggestions and knowledge base.

Sincerely,

Stephan Watkins


> -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] Re: Data Analysis

2012-04-20 Thread lloyd riggs

Dear Justin,

Dont panic.

1) there in cyclic happening at 1/4 the entire run but offset by 2-6 
picosecounds between runs.

2) There calculated PMF but the data comes from the origional pullf.xvg files 
generated if I look at each point (same thing a - or low pullf point.)

-This is precluding the first 2 picosecounds of a 4 ns pulled run as done by 
another group with similar (90% identical) protein sets (published).

-also in a few after the peak change in energy is reached (around 3.8 ns), I do 
see fluctuations which I expect due to more free movements.

-I also calculated everything with a single histogram analysis, then did 
statistics using ploting sofware (qti) for all runs together.  The errors are 
the same in either case.

-In the end the finalized data (means at any point overall, distances, etc...) 
are all the same and fit values.  If I exclude the data points I get smooth 
curves.  If I include them the single point from one of 11 or 1 of 10 runs just 
seems to effect the error analysis (STD deviation, Standard error) but affects 
the mean(s) very little.  In the end the mean is all that anyone cares about, 
along with other associated analysis, but I woundered.

-The errors in half the case ( say around 30 points in all across 22,000 or 
20,000 points) are just the mean of the previous and next point but with a 
negative sign?  In the other half they are always numbers very close to zero 
(ex: 0.002484890) with the prior or next point around say 30-40.

-The models dont show any wierdness if I print out the pdb for those frames in 
VMD, so do not know where the error is.  I dont know if its a spring effect, 
which I assume not if the force is constant, as the pull force is artificial, 
but I could see it causing a spring effect if the protein(s) one tries to pull 
apart are strongly bound together (ie say force equivalent in some way to the 
pull force applied).

Pretty much thats about it.

Stephan Lloyd Watkins

 Original-Nachricht 
> Datum: Fri, 20 Apr 2012 07:35:42 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re: Data Analysis

> 
> 
> lloyd riggs wrote:
> > Dear All,
> > 
> > A question about data analysis.  When Generating raw .xvg files of
> energies I
> > have found say 3-4 points out of 2000 (per run 11 total) is erroneous.
> > 
> > something like
> > 
> >> 20.43534
> > 21.7657 22.212 -34.88 23.680
> > 
> > Something like that.
> > 
> 
> Where are these data from, and how did you conclude that the offending
> point was
> erroneous?
> 
> > Now is there a routine in handling these?  I found when integrating all
> 11 it
> > makes several points error calculations double or triple at a single
> point.
> > Is it proper to remove these when submitting something to generate the
> smooth
> > curve, or are we supposed to include these?
> > 
> 
> You can't just throw away data you don't like without a more rigorous 
> statistical analysis.  You should investigate the source of the weird
> point(s) 
> to see if they might, in fact, be legitimate or generated by an error
> somewhere.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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[gmx-users] Re: Data Analysis

2012-04-20 Thread lloyd riggs


Dear All,

A question about data analysis.  When Generating raw .xvg files of energies I 
have found say 3-4 points out of 2000 (per run 11 total) is erroneous.

something like

> 20.43534
  21.7657
  22.212
  -34.88
  23.680

Something like that.

Now is there a routine in handling these?  I found when integrating all 11 it 
makes several points error calculations double or triple at a single point. Is 
it proper to remove these when submitting something to generate the smooth 
curve, or are we supposed to include these?

Grüess

Stephan Watkins
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Re: [gmx-users] Re: : Extending run append

2012-04-20 Thread lloyd riggs

Dear Dr. Abrahams,

I tried to re-create the issue per another e-mail and someone has since fixed 
the problem as it gives no errors now?  I wish I could say what the problem 
was, but as I dint fix it I have no clue.

The origional command was:

 qsub -M stephan.watk...@insel.ch -cwd -V -l h_cpu=200:00:00 -l h_vmem=6G -pe 
mpi 24 -r yes -R yes -b yes mpirun mdrun_mpi_d -s 
$HOME/21a_20/traj_7/traj_7.tpr -cpi state_prev.cpt -append -compact

And the error message: (trying from memory)

5 of seven files not found

--When I looked at the log, it looked for the varied files such as energy.edr, 
.xtc , .trr but could not find them.

Thats about it.

Gutten Tag,

Stephan Watkins
 Original-Nachricht 
> Datum: Fri, 20 Apr 2012 12:44:13 +1000
> Von: Mark Abraham 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re: : Extending run append

> On 20/04/2012 1:45 AM, lloyd riggs wrote:
> > Dear All,
> >
> > Another error here with Gromacs
> >
> > The append from continuing runs does not work.  It complains that
> several files are missing.  When I try to give it the files in the working 
> DIR or
> direct paths, it still gives the same complaint.
> >
> > I woundered if such a thing could also be a compilation time error, or
> something else.
> 
> Not likely. User error or file system issue are the most likely 
> explanations, but we have nowhere near enough information to help.
> 
> Mark
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[gmx-users] Re: : Extending run append

2012-04-19 Thread lloyd riggs


Dear All,

Another error here with Gromacs

The append from continuing runs does not work.  It complains that several files 
are missing.  When I try to give it the files in the working DIR or direct 
paths, it still gives the same complaint.

I woundered if such a thing could also be a compilation time error, or 
something else.

Sincerely,

Stephan Lloyd Watkins
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Re: [gmx-users] Re:WHAM question

2012-04-19 Thread lloyd riggs



 Original-Nachricht 
> Datum: Wed, 18 Apr 2012 10:49:00 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:WHAM question

> 
> 
> lloyd riggs wrote:
> >> When accusing the code of doing something wrong, "I don't know" isn't a
> >> >very good justification ;)  The contents of pullx.xvg are the COM
> >> >Acoordinates of the reference group on the axis or axes along which
> the
> >> >restraint was applied, followed by the distance between the reference
> and
> >> >pulled group, again along each axis.  In your case you should have the
> >> y->coordinate of the COM of the reference, and dY, which represents the
> >> >distance between the two groups along the y-axis only.  These values
> >> >should be easy to confirm with g_traj and g_dist.
> > 
> > My pullx.xvg file, as I think I mentioned, prints the refernce
> coordinates
> > and the coordinates of the COM of the pulled group.  I can in a spread
> sheet
> > (minus the reformating 10 times) just make a column of the dY.
> > 
> > My question, do you or anyone know why it prints the reference and
> pulled COM
> > rather than the pulled COM and dY?  Can somone compile something that
> way, or
> > is it some bug or maybe just something to do with the N Y N vs. N N Y
> > pulling?
> > 
> 
> The content of pullx.xvg (according to the headers and the explanations I
> have 
> seen) is indeed the COM of the reference and dY, not the coordinate(s) of
> the 
> pulled group.  Does g_dist contradict these assertions?  I am basing my 
> knowledge on its contents based on the printed header and statements from
> the 
> developers, but if something has gone wrong here, it's an important
> (potential) 
> bug to fix.
> 
> -Justin
> 

Dear Justin,

I tried it once, yes g_dist contradicts it well and gives the actual distances 
dy between the COMs.  Also, If I (I did this weeks back) use I think g_analyze 
or the utility which gives coordinates, print out the Y coordinates for the COM 
of the pulled group and it is the secound column printed to the pullx.xvg file. 
 The Gromacs instillation has been taken ove by the Chem/Computer admin so they 
are now responsible for it.  I also have it on my home PC, but can only use 
auxillary analysis scripts as it would take 1 year to run something unless I 
ported things to openCL, which would probably take me personally XX years.  I 
think however I am the only one using Gromacs here except for a 1 or 2 times a 
year course from the chem departmentas the problem is only with the 
instillation here I dont know if it is a bug, or maybe an instillation problem, 
or something else (seems like only a 2 line get and print to file thing could 
do that though, or it skips the A-B=delta portion of
  the script which I have no clue where is located?)

Sincerely,

Stephan Watkins





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

2012-04-18 Thread lloyd riggs

>When accusing the code of doing something wrong, "I don't know" isn't a >very 
>good justification ;)  The contents of pullx.xvg are the COM >Acoordinates of 
>the reference group on the axis or axes along which the >restraint was 
>applied, followed by the distance between the reference and >pulled group, 
>again along each axis.  In your case you should have the y->coordinate of the 
>COM of the reference, and dY, which represents the >distance between the two 
>groups along the y-axis only.  These values >should be easy to confirm with 
>g_traj and g_dist.

My pullx.xvg file, as I think I mentioned, prints the refernce coordinates and 
the coordinates of the COM of the pulled group.  I can in a spread sheet (minus 
the reformating 10 times) just make a column of the dY.

My question, do you or anyone know why it prints the reference and pulled COM 
rather than the pulled COM and dY?  Can somone compile something that way, or 
is it some bug or maybe just something to do with the N Y N vs. N N Y pulling?

Stephan Watkins



> -- 
> 
> 
> 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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