date:20110622




Shay Teaching wrote:

Hi everyone,

Does the appending option also work when doing PMF?
I have a simulation that crashed in the middle (not-gromacs-related), 
and now I want to continue from where it stopped.
But using the -append option does not seem to continue writing to the 
files specified in -px and -pf.




Appending can be done, but without seeing your actual series of commands, no one 
can offer you any useful advice or insight as to why it isn't working in your case.


-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] in preparation for 4.5.5 and 4.6 releases

2011-06-22 Thread Rossen Apostolov


Hi,

We are preparing for a new maintenance release 4.5.5. It will fix 
critical open issues with previous releases, so please file your reports 
in redmine.gromacs.org by the end of June.


After the 4.5.5 release, the stable branch will be frozen for bugfixes 
only, and new functionality will be added to a new release-4-6-patches 
branch, a fork of release-4-5-patches right after 4.5.5.


Currently the plan is to have in 4.6:

   * faster native GPU implementation supporting most of current
 Gromacs features
   * collective I/O
   * lambda dynamics and other free energy extensions
   * AdResS (http://www.mpip-mainz.mpg.de/~poma/multiscale/adress.php)
   * advanced rotational pulling
   * file history
   * several new tools
   * autoconf removed - support for building only with CMake

Code from contributors will be considered for inclusion also but it's 
necessary that


   * comes with support for the code in future releases, e.g. port it
 to the completely new C++ structure in the 5.0 release and
 maintain it after
   * builds against 4.5.5
   * produces scientifically reliable results
   * works in parallel and doesn't affect the performance
   * comes with regression test sets for the new features
   * has the necessary documentation for usage

After 4.5.5 bug fixes need to be applied as:

   * bugs in 4.5.5:
 o fix in 4.5.5 - fix in 4.6 - fix in master
   * bugs in the new features introduced in 4.6:
 o   fix in 4.6   - fix in master


The plan is to have 4.5.5 around end of July, and 4.6-gamma a month later.

Rossen
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[gmx-users] plateau in msd (glass transition); ref_t

2011-06-22 Thread Anja Kuhnhold

Hi everyone,

I'm simulating a bead-spring polymer model (1600 chains and 10 beads per chain 
in a 26.6^3 box with pbc) with LJ and FENE potentials.
I calculate the mean-square-displacement for different temperatures. For T=0.46 
(in LJ units) I expected to get a plateau in the msd curve (glass transition)- 
but there is none. The curve for T=0.46 is similar to the one for T=1.0 (above 
glass transition) with only a small shift to lower values- but no plateau.

My .mdp-files look as follows:

integrator  = md-vv
dt  = 0.0035
nsteps  = 100
nstxout = 1
nstvout = 1
nstfout = 1
nstlog  = 1
ns_type = grid
pbc = xyz
periodic_molecules  = yes
rvdw= 1.12
rlist   = 1.3
tcoupl  = nose-hoover
tc-grps = System
tau_t   = 20
ref_t   = 55.32
vdwtype = Shift
rcoulomb= 1.12
coulombtype = Reaction-Field-zero
epsilon_rf  = 0

I have 6 of these files, where only nsteps and nst*out are changed by 
multiplying them by 10 (so I get overlapping intervals for the msd).


Is the ref_t correct? The results in the md.log file say T is about 89.
Why do I not get a plateau? What did I not consider?

Thanks in advance.
Anja
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Re: [gmx-users] Programs to add residues

2011-06-22 Thread Michael Lerner

On Tue, Jun 21, 2011 at 4:12 PM, Chris Neale chris.ne...@utoronto.cawrote:

Try Loopy. You can get it to build termini in addition to loops.

http://wiki.c2b2.columbia.edu/**honiglab_public/index.php/**Software:Loopyhttp://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy

I've also seen people use PyMOL's builder to do this. Either way, you'll
need to take (a lot of) extra care to minimize your linker and make sure
that it looks reasonable.

-Michael

Nevertheless, I'd suggest simply omitting that part of the protein and
capping your new terminus to remove the charge. You will have more
difficulties converging the conformation of the unstructured terminus than
you may expect.

CHris.

-- original message --

Hi all,

Is there a program that allows the user to add residues to the N and C
terminus, without using the electron density? I would like to add a
short linker to my protein which doesn't exist in the electron
density.

Thanks a lot,

Sincerely,
Zack

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Re: [gmx-users] Autocorrelation of dipole moment

2011-06-22 Thread André Farias de Moura

sure, the ACF for a vector gives you the average cosine between that vector
at time t=0 and the same vector at a later time lag, thus negative values may
be seen as an inversion of the direction to which the vector points
out (-1 would
be the value for a vector lying 180 degrees away from the direction at t=0).

best

Andre

On Tue, Jun 21, 2011 at 8:29 PM, Chathurika Abeyrathne
c.abeyrat...@student.unimelb.edu.au wrote:


 Hi,

 Is it possible to get negative values for normalized autocorrelation of
 total dipole moment.

 Thank you.


 Regards,
 Chathurika.

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Re: [gmx-users] Questions about GB parameters




Per Larsson wrote:

Hi!

I did some digging and think I can clarify at least the first question.

Sorry for the confusion with regard to the earlier post. What is specified in
the gbsa.itp file under the gbr column is indeed vdW-radii. These are used to
compute Born radii, as the manual says. The dielectric offset is subtracted
from the vdW radii, as this has been shown to improve the agreement between
PB and GB calculations (see eg. the OBC-paper, Onufriev, Bashford and Case,
Proteins, 55, 383-394).



Thanks, that makes sense then.  The code and .mdp settings indeed reflect this. 
 I've updated the git manual to accurately describe this.



For the second question, I am a little confused myself now. The values found
in the gbsa.itp-file are exactly those found in the Tinker package (in the
ksolv.f-routine), which also cites the same reference. Hmm...I'll be back
again for this one.



I look forward to it :)

-Justin


Cheers /Per


21 jun 2011 kl. 18.42 skrev Justin A. Lemkul:


Can anyone comment further on either of these issues?

-Justin

Mark Abraham wrote:

On 15/06/2011 4:24 AM, Justin A. Lemkul wrote:

Hi All,

I wanted to dig up an old discussion that hit the list a long time ago
because I'm now encountering some problems understanding the GB
settings myself.  The discussion in question is here:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html

I wanted to post a couple of questions based on Per's response.

1. Based on that post, it seems to me that the value in the gbr column
should have a dielectric offset added to it during the GB calculations.
In the code, though (genborn.c, around line 484 in the latest
release-4-5-patches), it looks like the dielectric offset is
subtracted, not added.  I guess the code is reversing the process,
going from GB radius back to vdW radius by subtracting the dielectric
offset?  It seems, then, that the parameters in gbsa.itp should specify
GB radii, not vdW radii, though the manual says the gbr column is
atomic van der Waals radii, which are used in computing the Born
radii.  Is the opposite actually true?

It does look to me as though something is mis-sense here. The quantity
given in gb_dielectric_offset is always subtracted from a value that I
think is found in the gbr column of [implicit_genborn_parameters]. Mark

2. I am still unclear on the source of the HCT scaling factors.  From
the reference cited in the manual, it would seem that scaling factors
are interaction-dependent, at least when H atoms are concerned.  I also
cannot find any indication of where these values came from.  None of
the values of Table 2 in the HCT reference match the contents of the
hct column.  Again I wonder if I'm missing something obvious :)

Thanks for any insight!

-Justin


-- 

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

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


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[gmx-users] restraints in PMF (Justin's tutorial)

2011-06-22 Thread Rebeca García Fandiño

Hello,

I am trying to obtain the PMF from Umbrella Sampling of the process of
separating two monomers of a dimer, following Justin 's
tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

I have done the Umbrella Sampling simulations without using any restraints in
any of the monomers, however, I can see that they move and gyrate so that
although the c.o.m are separated from each other, there are parts of both
interacting, in such way that they are not separated as they should be.

Would it be correct if I apply restraints to both monomers in all the Umbrella
Sampling simulations?. I have seen that in Justin's tutorial they applied
restraints to one of the chains, but in my case I think I will need to restrain
both of the units. Would that be correct for the PMF calculation?

Thanks a lot in advance.

Rebeca.

Date: Mon, 20 Jun 2011 17:03:56 -0400
From: jalem...@vt.edu
To: rega...@hotmail.com
CC: gmx-users@gromacs.org
Subject: Re: doubt about your Umbrella Sampling tutorial

Rebeca García Fandiño wrote:
Dear Justin,
my name is Rebeca and I am a postdoctoral student in Santiago de
Compostela University. Sorry for disturbing you to your personal mail, I
have tried to post to the Gromacs-list first, but I did not get any answer.

I was traveling and not paying much attention to messages across the list. I
will CC this reply to the list in the hopes that it is useful to others, as
well.

I am trying to obtain the PMF from Umbrella Sampling of the process of
separating two monomers of a dimer, following your tutorial, and I have
a pair of doubts:

1)In this tutorial the generation of configurations is done using a .mdp
file for pulling one chain from another, but is it possible to generate
the configurations for Umbrella Sampling by hand, I mean, changing the
z coordinate of the monomer I want to move, then solvating and then
minimizing these configurations? Is there any problem with this protocol
for the obtaining of the configurations?

No problem at all. The tutorial is but one possible method.

2) I have noticed that you use restraints in the md_umbrella.mdp for the
fixed chain. Is that correct? I can understand the restraints in the
pulling simulations for generate starting configurations, but once you
have the configurations, is is necessary to restrain one part of the
system?

Not usually. The tutorial presents a special case.

Thanks a lot in advance for your help with this topic, and thank you
very much also for publishing this interesting tutorial. There was
nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I
think it is more than wellcome for all Gromacs users!

Glad they're useful :)

-Justin

Best wishes,
Rebeca.

Dr. Rebeca García Fandiño
Department of Organic Chemistry and Center for Research in Biological
Chemistry
and Molecular Materials
Santiago de Compostela University
E-15782 Santiago de Compostela (Spain)
e-mail: rebeca.garcia.fand...@usc.es
Phone: 34-981563100 ext 15760

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] restraints in PMF (Justin's tutorial)

Rebeca García Fandiño wrote:

Hello,
I am trying to obtain the PMF from Umbrella Sampling of the process of
separating two monomers of a dimer, following Justin 's tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

I have done the Umbrella Sampling simulations without using any
restraints in any of the monomers, however, I can see that they move and
gyrate so that although the c.o.m are separated from each other, there
are parts of both interacting, in such way that they are not separated
as they should be.

Would it be correct if I apply restraints to both monomers in all the
Umbrella Sampling simulations?. I have seen that in Justin's tutorial
they applied restraints to one of the chains, but in my case I think I
will need to restrain both of the units. Would that be correct for the
PMF calculation?

There are no position restraints applied during the umbrella sampling
simulations. They are unnecessary. The umbrella potential is itself a
restraint to maintain COM separation.

If parts of your proteins are interacting, you simply haven't fully separated
your monomers and you need to create configurations with greater COM separation.
If you apply position restraints to fit some notion that your monomers
shouldn't interact at certain distances, then you're applying an unnatural (and
potentially incorrect) bias, causing the PMF to converge incorrectly.

-Justin

Thanks a lot in advance.

Rebeca.

Date: Mon, 20 Jun 2011 17:03:56 -0400
From: jalem...@vt.edu
To: rega...@hotmail.com
CC: gmx-users@gromacs.org
Subject: Re: doubt about your Umbrella Sampling tutorial

Rebeca García Fandiño wrote:
Dear Justin,
my name is Rebeca and I am a postdoctoral student in Santiago de
Compostela University. Sorry for disturbing you to your personal
mail, I
have tried to post to the Gromacs-list first, but I did not get any
answer.

I was traveling and not paying much attention to messages across the
list. I
will CC this reply to the list in the hopes that it is useful to
others, as well.

I am trying to obtain the PMF from Umbrella Sampling of the process of
separating two monomers of a dimer, following your tutorial, and I
have

a pair of doubts:

z coordinate of the monomer I want to move, then solvating and then
minimizing these configurations? Is there any problem with this
protocol

for the obtaining of the configurations?

No problem at all. The tutorial is but one possible method.

2) I have noticed that you use restraints in the md_umbrella.mdp
for the

fixed chain. Is that correct? I can understand the restraints in the
pulling simulations for generate starting configurations, but once you
have the configurations, is is necessary to restrain one part of the
system?

Not usually. The tutorial presents a special case.

Glad they're useful :)

-Justin

Best wishes,
Rebeca.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)

2011-06-22 Thread udaya kiran marelli

Dear Mark Abraham,

Thank you for the reply.  However, I am sorry to tell you that I could not
find a tutorial that really is explicit to explain the procedure.  Could you
please suggest some tutorial covering the non-water solvent box generation
and optimization using all-atom charmm force-field on GROMACS.

best regards,
Uday.


On Tue, Jun 21, 2011 at 4:05 AM, gmx-users-requ...@gromacs.org wrote:

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 Today's Topics:

   1. Re: NVT equilibration of DMSO solvent (Charmm all-atomforce
  field) (Mark Abraham)
   2. Re: EM broke protein-lipid system (Mark Abraham)
   3. Re: doubt about your Umbrella Sampling tutorial (Justin A. Lemkul)
   4. Re: minimum image violation (Justin A. Lemkul)
   5. Re: error bars g_wham (Justin A. Lemkul)
   6. NMR chemical shift restraints (Thomas Evangelidis)
   7. Re: NMR chemical shift restraints (Mark Abraham)
   8. Re: Increase in charge after adding the ligand (bharat gupta)


 --

 Message: 1
 Date: Tue, 21 Jun 2011 03:51:53 +1000
 From: Mark Abraham mark.abra...@anu.edu.au
 Subject: Re: [gmx-users] NVT equilibration of DMSO solvent (Charmm
all-atomforce field)
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 4dff88b9.4080...@anu.edu.au
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 On 21/06/2011 2:44 AM, udaya kiran marelli wrote:
  Dear GROMACS users,
 
  I have generated a 4*4*4 octahedral DMSO box containing 64 molecules
  (Charmm all-atom force field) which need to be NVT equilibrated in
  order to pass it for usage in genbox.  Could one of you provide info
  on how to do the NVT and periodic boundary equilibration to remove the
  residual ordering of the solvent?

 Most tutorials will cover the details of such stages well.

 Mark


 --

 Message: 2
 Date: Tue, 21 Jun 2011 03:54:57 +1000
 From: Mark Abraham mark.abra...@anu.edu.au
 Subject: Re: [gmx-users] EM broke protein-lipid system
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 4dff8971.2010...@anu.edu.au
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 On 21/06/2011 2:46 AM, Du Jiangfeng (BIOCH) wrote:
  Dear Gromacs Users,
  It comes to me with million problems per day during I am using gromacs.
 :(

 Computational chemistry is rarely easy. The tasks are complex and
 demanding, even when the software is mature and the documentation well
 written... That said, you're tackling a difficult multi-phase system...

  Maybe you are the right persons i should ask about coarse grained
 protein-lipid simulation. Right now I have a system with a bilayer (DOPCs)
 and a protein (Histone). After EM simulation, it worked quite well Then,
 this system was filled with water and was performed by EM again. Then it was
 scattered severely. Though I tried lipid constraint and many other methods,
 the problem is still here
  Any suggestions?

 I can only suggest that you find and follow suitable tutorial material,
 simplifying your system as much as you can, adding complexity in stages.

 Mark


 --

 Message: 3
 Date: Mon, 20 Jun 2011 17:03:56 -0400
 From: Justin A. Lemkul jalem...@vt.edu
 Subject: [gmx-users] Re: doubt about your Umbrella Sampling tutorial
 To: Rebeca Garc?a Fandi?o rega...@hotmail.com
 Cc: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 4dffb5bc.1060...@vt.edu
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed



 Rebeca García Fandiño wrote:
  Dear Justin,
  my name is Rebeca and I am a postdoctoral student in Santiago de
  Compostela University. Sorry for disturbing you to your personal mail, I
  have tried to post to the Gromacs-list first, but I did not get any
 answer.

 I was traveling and not paying much attention to messages across the list.
  I
 will CC this reply to the list in the hopes that it is useful to others, as
 well.

  I am trying to obtain the PMF from Umbrella Sampling of the process of
  separating two monomers of a dimer, following your tutorial, and I have
  a pair of doubts:
 
  1)In this tutorial the generation of configurations is done using a .mdp
  file for pulling one chain from another, but is it possible to generate
  the configurations for Umbrella Sampling by hand, I mean, changing the
  z coordinate of the monomer I want to move, then solvating and then
  minimizing these configurations? Is there any problem with this protocol
  for

RE: [gmx-users] restraints in PMF (Justin's tutorial)

2011-06-22 Thread Rebeca García Fandiño


Thanks a lot for your quick answer!

I think they are separated enough, however my monomers are cyclic (like 
discs); I start with a parallel conformation between then, but along the
 Umbrella simulation, both of them rotate and approach.
If I do not use restraints, how could I avoid the rotation?

I am using the following md_umbrella.mdp:

title   = Umbrella pulling simulation
define  = 
define  =
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50   ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000 
nstvout = 5000
nstfout = 5000
nstxtcout   = 5000 
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = r_1_r_2  CL3
tau_t   = 0.5   0.5
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

Thanks a lot again for your help.

Best wishes,

Rebeca.

 Date: Wed, 22 Jun 2011 10:53:16 -0400
 From: jalem...@vt.edu
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial)
 
 
 
 Rebeca García Fandiño wrote:
  Hello,
  I am trying to obtain the PMF from Umbrella Sampling of the process of 
  separating two monomers of a dimer, following Justin 's tutorial
  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
  
  I have done the Umbrella Sampling simulations without using any 
  restraints in any of the monomers, however, I can see that they move and 
  gyrate so that although the c.o.m are separated from each other, there 
  are parts of both interacting, in such way that they are not separated 
  as they should be.
  
  Would it be correct if I apply restraints to both monomers in all the 
  Umbrella Sampling simulations?. I have seen that in Justin's tutorial 
  they applied restraints to one of the chains, but in my case I think I 
  will need to restrain both of the units. Would that be correct for the 
  PMF calculation?
  
 
 There are no position restraints applied during the umbrella sampling 
 simulations.  They are unnecessary.  The umbrella potential is itself a 
 restraint to maintain COM separation.
 
 If parts of your proteins are interacting, you simply haven't fully separated 
 your monomers and you need to create configurations with greater COM 
 separation. 
   If you apply position restraints to fit some notion that your monomers 
 shouldn't interact at certain distances, then you're applying an unnatural 
 (and 
 potentially incorrect) bias, causing the PMF to converge incorrectly.
 
 -Justin
 
  Thanks a lot in advance.
  
  Rebeca.
  
Date: Mon, 20 Jun 2011 17:03:56 -0400
From: jalem...@vt.edu
To: rega...@hotmail.com
CC: gmx-users@gromacs.org
Subject: Re: doubt about your Umbrella Sampling tutorial
   
   
   
Rebeca García Fandiño wrote:
 Dear Justin,
 my name is Rebeca and I am a postdoctoral student in Santiago de
 Compostela University. Sorry for disturbing you to your personal 
  mail, I
 have tried to post to the Gromacs-list first, but I did not get any 
  answer.
   
I was traveling and not paying much attention to messages across the 
  list. I
will CC this reply to the list in the hopes that it is useful to 
  others, as well.
   
 I am trying to obtain the PMF from Umbrella Sampling of the process of
 separating two monomers of a dimer, following your tutorial, and I 
  have
 a pair of doubts:

 1)In this tutorial the generation of configurations is done using a 
  .mdp
 file for pulling one chain from another, but is it possible to 
  generate
 the configurations for Umbrella Sampling by hand, I mean, 
  changing the
 z coordinate of the monomer I want to move, then solvating and then
 minimizing these configurations? Is there any problem with this 
  protocol
 for the obtaining of the configurations?

Re: [gmx-users] restraints in PMF (Justin's tutorial)




Rebeca García Fandiño wrote:

Thanks a lot for your quick answer!
I think they are separated enough, however my monomers are cyclic (like 
discs); I start with a parallel conformation between then, but along the 
Umbrella simulation, both of them rotate and approach.

If I do not use restraints, how could I avoid the rotation?



You don't.  Why wouldn't two molecules rotate freely in solution when binding or 
unbinding?  It seems like completely natural behavior.  Even in simple systems 
of protein-ligand association, part of the binding energy is the entropic 
restriction of the ligand into a certain binding-competent pose.  Why wouldn't 
that happen here?  Sounds like an artificial notion to me.


-Justin


I am using the following md_umbrella.mdp:

title   = Umbrella pulling simulation
define  =
define  =
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50   ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000
nstvout = 5000

nstfout = 5000
nstxtcout   = 5000
nstenergy   = 5000

; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = r_1_r_2  CL3
tau_t   = 0.5   0.5
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

Thanks a lot again for your help.

Best wishes,

Rebeca.


  Date: Wed, 22 Jun 2011 10:53:16 -0400
  From: jalem...@vt.edu
  To: gmx-users@gromacs.org
  Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial)
 
 
 
  Rebeca García Fandiño wrote:
   Hello,
   I am trying to obtain the PMF from Umbrella Sampling of the process of
   separating two monomers of a dimer, following Justin 's tutorial
   
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

  
   I have done the Umbrella Sampling simulations without using any
   restraints in any of the monomers, however, I can see that they 
move and

   gyrate so that although the c.o.m are separated from each other, there
   are parts of both interacting, in such way that they are not separated
   as they should be.
  
   Would it be correct if I apply restraints to both monomers in all the
   Umbrella Sampling simulations?. I have seen that in Justin's tutorial
   they applied restraints to one of the chains, but in my case I think I
   will need to restrain both of the units. Would that be correct for the
   PMF calculation?
  
 
  There are no position restraints applied during the umbrella sampling
  simulations. They are unnecessary. The umbrella potential is itself a
  restraint to maintain COM separation.
 
  If parts of your proteins are interacting, you simply haven't fully 
separated
  your monomers and you need to create configurations with greater COM 
separation.

  If you apply position restraints to fit some notion that your monomers
  shouldn't interact at certain distances, then you're applying an 
unnatural (and

  potentially incorrect) bias, causing the PMF to converge incorrectly.
 
  -Justin
 
   Thanks a lot in advance.
  
   Rebeca.
  
Date: Mon, 20 Jun 2011 17:03:56 -0400
From: jalem...@vt.edu
To: rega...@hotmail.com
CC: gmx-users@gromacs.org
Subject: Re: doubt about your Umbrella Sampling tutorial
   
   
   
Rebeca García Fandiño wrote:
 Dear Justin,
 my name is Rebeca and I am a postdoctoral student in Santiago de
 Compostela University. Sorry for disturbing you to your personal
   mail, I
 have tried to post to the Gromacs-list first, but I did not get 
any

   answer.
   
I was traveling and not paying much attention to messages across the
   list. I
will CC this reply to the list in the hopes that it is useful to
   others, as well.
   
 I am trying to obtain the PMF from Umbrella Sampling of the 
process of

 separating two monomers of a dimer, following your tutorial, and I
   have
 a pair of doubts:

Re: [gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)




udaya kiran marelli wrote:


Dear Mark Abraham,

Thank you for the reply.  However, I am sorry to tell you that I could 
not find a tutorial that really is explicit to explain the procedure.  
Could you please suggest some tutorial covering the non-water solvent 
box generation and optimization using all-atom charmm force-field on 
GROMACS.




Please do not include the whole digest in your replies.  Cut and paste any 
relevant text and delete the rest.  Including the whole digest makes the archive 
terribly confusing.


To the point: there aren't going to be tutorials that cover every possible 
iteration of what someone wants to do.  Generate a reasonable starting 
configuration and equilibrate under an appropriate ensemble.  If you want 
explicit pointers on what may or may not be right or wrong with your .mdp 
settings, you need to post an .mdp file for comment.  Achieving a periodic 
system under NVT conditions is simple (and discussed in just about every 
tutorial, even if the goal of the tutorial is not explicitly what you want to 
do).  Set pbc = xyz and use the thermostat of your choice with no pressure 
coupling.  Presto - NVT ensemble.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

RE: [gmx-users] restraints in PMF (Justin's tutorial)

2011-06-22 Thread Rebeca García Fandiño

OK,
I will try to increase the distances of the c.o.m of both molecules to 
eliminate any contact between them, adding more windows.
Thanks a lot for your help!
Best wishes,
Rebeca.

 Date: Wed, 22 Jun 2011 11:51:36 -0400
 From: jalem...@vt.edu
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial)

 Rebeca García Fandiño wrote:
  Thanks a lot for your quick answer!
  I think they are separated enough, however my monomers are cyclic (like 
  discs); I start with a parallel conformation between then, but along the 
  Umbrella simulation, both of them rotate and approach.
  If I do not use restraints, how could I avoid the rotation?

 You don't.  Why wouldn't two molecules rotate freely in solution when binding 
 or 
 unbinding?  It seems like completely natural behavior.  Even in simple 
 systems 
 of protein-ligand association, part of the binding energy is the entropic 
 restriction of the ligand into a certain binding-competent pose.  Why 
 wouldn't 
 that happen here?  Sounds like an artificial notion to me.

 -Justin

  I am using the following md_umbrella.mdp:

  title   = Umbrella pulling simulation
  define  =
  define  =
  ; Run parameters
  integrator  = md
  dt  = 0.002
  tinit   = 0
  nsteps  = 50   ; 1 ns
  nstcomm = 10
  ; Output parameters
  nstxout = 5000
  nstvout = 5000
  nstfout = 5000
  nstxtcout   = 5000
  nstenergy   = 5000
  ; Bond parameters
  constraint_algorithm= lincs
  constraints = all-bonds
  continuation= yes
  ; Single-range cutoff scheme
  nstlist = 5
  ns_type = grid
  rlist   = 1.4
  rcoulomb= 1.4
  rvdw= 1.4
  ; PME electrostatics parameters
  coulombtype = PME
  fourierspacing  = 0.12
  fourier_nx  = 0
  fourier_ny  = 0
  fourier_nz  = 0
  pme_order   = 4
  ewald_rtol  = 1e-5
  optimize_fft= yes
  ; Berendsen temperature coupling is on in two groups
  Tcoupl  = Nose-Hoover
  tc_grps = r_1_r_2  CL3
  tau_t   = 0.5   0.5
  ref_t   = 300   300
  ; Pressure coupling is on
  Pcoupl  = Parrinello-Rahman
  pcoupltype  = isotropic
  tau_p   = 1.0
  compressibility = 4.5e-5
  ref_p   = 1.0
  ; Generate velocities is off
  gen_vel = no
  ; Periodic boundary conditions are on in all directions
  pbc = xyz
  ; Long-range dispersion correction
  DispCorr= EnerPres
  ; Pull code
  pull= umbrella
  pull_geometry   = distance
  pull_dim= N N Y
  pull_start  = yes
  pull_ngroups= 1
  pull_group0 = r_1
  pull_group1 = r_2
  pull_init1  = 0
  pull_rate1  = 0.0
  pull_k1 = 1000  ; kJ mol^-1 nm^-2
  pull_nstxout= 1000  ; every 2 ps
  pull_nstfout= 1000  ; every 2 ps

  Thanks a lot again for your help.

  Best wishes,

  Rebeca.

Date: Wed, 22 Jun 2011 10:53:16 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial)

Rebeca García Fandiño wrote:
 Hello,
 I am trying to obtain the PMF from Umbrella Sampling of the process of
 separating two monomers of a dimer, following Justin 's tutorial

  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

 I have done the Umbrella Sampling simulations without using any
 restraints in any of the monomers, however, I can see that they 
  move and
 gyrate so that although the c.o.m are separated from each other, there
 are parts of both interacting, in such way that they are not separated
 as they should be.

 Would it be correct if I apply restraints to both monomers in all the
 Umbrella Sampling simulations?. I have seen that in Justin's tutorial
 they applied restraints to one of the chains, but in my case I think I
 will need to restrain both of the units. Would that be correct for the
 PMF calculation?

There are no position restraints applied during the umbrella sampling
simulations. They are unnecessary. The umbrella potential is itself a
restraint to maintain COM separation.

If parts of your proteins are interacting, you simply haven't fully 
  separated
your monomers and you need to create configurations with greater COM 
  separation.
If you apply position restraints to fit some notion that your monomers
shouldn't interact at certain distances, then you're applying an 
  unnatural (and
potentially incorrect) bias, causing the PMF to converge incorrectly.

-Justin

 Thanks a lot in advance.

 Rebeca.

  Date: Mon, 20 Jun 2011 17:03:56 -0400
  From: jalem...@vt.edu
  To: rega...@hotmail.com
  CC: gmx-users@gromacs.org
  Subject: Re: doubt about your Umbrella Sampling tutorial

  Rebeca García Fandiño wrote:
   Dear

[gmx-users] restraints in PMF (Justin's tutorial)

2011-06-22 Thread chris . neale

Actually, this depends on what you are trying to achieve. If you  
simply want to obtain the standard binding free energy, and somehow  
you know that the bound state is represented by your umbrella at  
dist=0 (via a crystal structure, for example), then using additional  
restraints is common, acceptable, and in many cases desirable.


You can do this in analogy to, for example: D. L. Mobley, J. D.  
Chodera, K. A. Dill. On the use of orientational restraints and  
symmetry number corrections in alchemical free energy calculations,  
Journal of Chemical Physics 125:084902, 2006. Selected for the Virtual  
Journal of Biological Physics Research 12(5), 2006.


Since the free energy is a state function, you are free to select any  
pathway and it is useful to pick one that converges quickly... and  
those involving rotation of large molecules are sure to converge very  
slowly.


If you do this, then you'll need to account for the restraints in your  
free energy term in a way similar to that outlined in the paper that I  
referenced above.


The only reason that you would want to stick to the simple PMF is if  
you are actually interested in the shape of the unrestrained PMF, in  
which case you can't add additional restraints.


Chris.

-- original message --

Rebeca García Fandiño wrote:

Thanks a lot for your quick answer!
I think they are separated enough, however my monomers are cyclic  
(like discs); I start with a parallel conformation between then, but  
along the Umbrella simulation, both of them rotate and approach.

If I do not use restraints, how could I avoid the rotation?



You don't.  Why wouldn't two molecules rotate freely in solution when  
binding or

unbinding?  It seems like completely natural behavior.  Even in simple systems
of protein-ligand association, part of the binding energy is the entropic
restriction of the ligand into a certain binding-competent pose.  Why wouldn't
that happen here?  Sounds like an artificial notion to me.

-Justin


I am using the following md_umbrella.mdp:

title   = Umbrella pulling simulation
define  =
define  =
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50   ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000nstvout = 5000
nstfout = 5000
nstxtcout   = 5000nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = r_1_r_2  CL3
tau_t   = 0.5   0.5
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

Thanks a lot again for your help.

Best wishes,

Rebeca.


  Date: Wed, 22 Jun 2011 10:53:16 -0400
  From: jalemkul at vt.edu
  To: gmx-users at gromacs.org
  Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial)
 
 
 
  Rebeca García Fandiño wrote:
   Hello,
   I am trying to obtain the PMF from Umbrella Sampling of the process of
   separating two monomers of a dimer, following Justin 's tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

  
   I have done the Umbrella Sampling simulations without using any
   restraints in any of the monomers, however, I can see that they move and
   gyrate so that although the c.o.m are separated from each other, there
   are parts of both interacting, in such way that they are not separated
   as they should be.
  
   Would it be correct if I apply restraints to both monomers in all the
   Umbrella Sampling simulations?. I have seen that in Justin's tutorial
   they applied restraints to one of the chains, but in my case I think I
   will need to restrain both of the units. Would that be correct for the
   PMF calculation?
  
 
  There are no position restraints applied during the umbrella sampling
  simulations. They are unnecessary. The umbrella potential is itself a
  restraint to maintain COM separation.
 
  If parts of your proteins are

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 138

2011-06-22 Thread marco miele

...@gromacs.org
Message-ID: 4e01cd94.8050...@kth.se
Content-Type: text/plain; charset=utf-8

Hi,

We are preparing for a new maintenance release 4.5.5. It will fix
critical open issues with previous releases, so please file your reports
in redmine.gromacs.org by the end of June.

After the 4.5.5 release, the stable branch will be frozen for bugfixes
only, and new functionality will be added to a new release-4-6-patches
branch, a fork of release-4-5-patches right after 4.5.5.

Currently the plan is to have in 4.6:

* faster native GPU implementation supporting most of current
Gromacs features
* collective I/O
* lambda dynamics and other free energy extensions
* AdResS (http://www.mpip-mainz.mpg.de/~poma/multiscale/adress.php)
* advanced rotational pulling
* file history
* several new tools
* autoconf removed - support for building only with CMake

Code from contributors will be considered for inclusion also but it's
necessary that

* comes with support for the code in future releases, e.g. port it
to the completely new C++ structure in the 5.0 release and
maintain it after
* builds against 4.5.5
* produces scientifically reliable results
* works in parallel and doesn't affect the performance
* comes with regression test sets for the new features
* has the necessary documentation for usage

After 4.5.5 bug fixes need to be applied as:

* bugs in 4.5.5:
o fix in 4.5.5 - fix in 4.6 - fix in master
* bugs in the new features introduced in 4.6:
o fix in 4.6 - fix in master

The plan is to have 4.5.5 around end of July, and 4.6-gamma a month later.

Rossen
-- next part --
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Message: 4
Date: Wed, 22 Jun 2011 13:34:58 +0200
From: Anja Kuhnhold anja.kuhnh...@physik.uni-halle.de
Subject: [gmx-users] plateau in msd (glass transition); ref_t
To: gmx-users@gromacs.org
Message-ID: fac78671a57f.4e01e...@uni-halle.de
Content-Type: text/plain; charset=us-ascii

Hi everyone,

I'm simulating a bead-spring polymer model (1600 chains and 10 beads per
chain in a 26.6^3 box with pbc) with LJ and FENE potentials.
I calculate the mean-square-displacement for different temperatures. For
T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass
transition)- but there is none. The curve for T=0.46 is similar to the one
for T=1.0 (above glass transition) with only a small shift to lower values-
but no plateau.

My .mdp-files look as follows:

integrator = md-vv
dt = 0.0035
nsteps = 100
nstxout = 1
nstvout = 1
nstfout = 1
nstlog = 1
ns_type = grid
pbc = xyz
periodic_molecules = yes
rvdw= 1.12
rlist = 1.3
tcoupl = nose-hoover
tc-grps = System
tau_t = 20
ref_t = 55.32
vdwtype = Shift
rcoulomb= 1.12
coulombtype = Reaction-Field-zero
epsilon_rf = 0

I have 6 of these files, where only nsteps and nst*out are changed by
multiplying them by 10 (so I get overlapping intervals for the msd).

Is the ref_t correct? The results in the md.log file say T is about 89.
Why do I not get a plateau? What did I not consider?

Thanks in advance.
Anja

Message: 5
Date: Wed, 22 Jun 2011 08:52:32 -0400
From: Michael Lerner mgler...@gmail.com
Subject: Re: [gmx-users] Programs to add residues
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: banlktim7dby4uwefcc38hipjw8tz7jz...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1

On Tue, Jun 21, 2011 at 4:12 PM, Chris Neale chris.ne...@utoronto.ca
wrote:

Try Loopy. You can get it to build termini in addition to loops.

http://wiki.c2b2.columbia.edu/**honiglab_public/index.php/**Software:Loopy
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy

I've also seen people use PyMOL's builder to do this. Either way, you'll
need to take (a lot of) extra care to minimize your linker and make sure
that it looks reasonable.

-Michael

CHris.

-- original message --

Hi all,

Thanks a lot,

Sincerely,
Zack

--
gmx-users mailing listgmx

Re: [gmx-users] DPPC temperatur setting




marco miele wrote:

Please heed this:


When replying, please edit your Subject line so it is more specific
than Re: Contents of gmx-users digest...



...and don't reply to the entire digest.  I just stated the reasons a few 
minutes ago and won't bother to repeat myself again here.


snip


marco miele wrote:
  Hi everybody
  I am starting to analyze the membrane system composed with DPPC
lipids,
  I saw  both MD membrane paper and KALP-15 tutorial to setting a 323K.
  My question is That
  in this way we working around 50 C, which is not body temperature
37 C,
  this is not realistic approach,
  If my interest is to obtain data that respects the human body
condition
  can I to setting the temperature at 310 = 37 C or a make mistake and
  obtain artefacts data.
 

The reason for using 323 K in the case of DPPC is that (1) it is a
common
experimental temperature and (2) it is above the phase-transition
temperature
for this lipid.  Anywhere below 315 K or so and your membrane will
enter a gel
phase, which is not representative of the membrane properties in
vivo.  Working
with DPPC thus involves a tradeoff - you can either produce a liquid
phase (like
in vivo) or physiological temperature (while losing the physical
properties
associated with cellular membranes).  The latter is often
disfavored, but the
end result is that DPPC is simply a poor choice to represent cell
membranes, but
is often a useful in vitro model, depending on your aims and
available data.

-Justin


 
My aim is to obtain a good model for analyzing a receptor protein (not 
channel).
I prepared a system with DPPC CHOL and Protein, but  I am not sure fore 
only temperature.


The latter is often disfavored, but the end result is that DPPC is 
simply a poor choice to represent cell membranes,
but is often a useful in vitro model, depending on your aims and 
available data.


What kind of lipid you suggest me, in vision of system indicated before 
DPPC CHOL PROTEIN.
I am interesting to understand if the conformation of protein is 
mantained in diff % of CHOL.




Well, if you're convinced you want to model DPPC/cholesterol membranes, then I'm 
not going to try to suggest you do anything else.  Only you know what your goals 
are and what experimental observables you're trying to reproduce or expand upon. 
 A DPPC/cholesterol mixture does not represent human cell membranes very well, 
but this information is specific to different cell types.


If you just want to measure the effects of cholesterol on some arbitrary lipid 
model, then it doesn't much matter what you use, but you'll have to deal with 
the assumption that pure DPPC would inherently be in the gel phase in vivo. 
Cholesterol will augment this effect, so it is hard to say what temperature you 
should use.  If you state the assumption that pure DPPC should be simulated at 
roughly 323 K and everything is relative to that, it's part of the 
interpretation of your results.


-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] Timing variability

2011-06-22 Thread chris . neale


Dear Users:

Has anybody else looked at simulation speed (ns/day) over the segments  
of long runs? I always benchmark and optimize my systems carefully,  
but it was only recently that I realized how much variability I am  
obtaining over long runs. Perhaps this is specific to my cluster,  
which is one reason for my post.


Here is the performance (in ns/day) that I obtain with a single run.  
This is representative of what I see with 30 other runs (see list  
below). First, the distribution is bimodal, with peaks at around 80  
and 90 ns/day. Second, the values go as low as 70 ns/day (and I have  
seen as low as 50 ns/day when I look through all 30 run directories  
that differ only by the position of the umbrella restraint).


I am using gromacs 4.5.3 and I run it like this:
mpirun mdrun_mpi -deffnm md1 -dlb yes -npme 16 -cpt 30 -maxh 47 -cpi  
md1.cpt -cpo md1.cpt -px coord.xvg -pf force.xvg -noappend


I have obtained similar behaviour also with another system.

I have attempted to correlate timing with the node on which the job  
runs, the output of the ^Grid: in the .log file, the DD division of  
PME and real-space and the value of pme mesh/force, all to no avail. I  
have found one correlation whereby the very slow runs also indicate a  
high relative load for PME.


I suspect that it is some value that is being determined at run start  
time that is affecting my performance, but I am not sure what this  
could be. Perhaps the fourier-spacing is leading to different initial  
grids?


Thank you (timing information and my .mdp file follows),
Chris

### Output the ns/day obtained by the run segments
$ grep Perf *log|awk '{print $4}'

78.286
82.345
81.573
83.418
92.423
90.863
85.833
91.131
91.820
71.246
76.844
91.805
92.037
85.702
92.251
89.706
88.590
89.381
90.446
81.142
76.365
76.968
76.037
79.286
79.895
79.047
78.273
79.406
78.018
78.645
78.172
80.255
81.032
81.047
77.414
78.414
80.167
79.278
80.892
82.796
81.300
77.392
71.350
73.134
76.519
75.879
80.684
81.076
87.821
90.064
88.409
80.803
88.435

### My .mdp file

constraints = all-bonds
lincs-iter =  1
lincs-order =  6
constraint_algorithm =  lincs
integrator = sd
dt = 0.004
tinit = 100
init_step=  0
nsteps = 10
nstcomm = 1
nstxout = 10
nstvout = 10
nstfout = 10
nstxtcout = 25000
nstenergy = 25000
nstlist = 5
nstlog=0 ; reduce log file size
ns_type = grid
rlist = 1
rcoulomb = 1
rvdw = 1
coulombtype = PME
ewald-rtol = 1e-5
optimize_fft = yes
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
tc_grps =  System
tau_t   =  1.0
ld_seed =  -1
ref_t = 300
gen_temp = 300
gen_vel = yes
unconstrained_start = no
gen_seed = -1
Pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 4 4
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0

; COM PULLING
pull = umbrella
pull_geometry= position
pull_dim = N N Y
pull_start   = no
pull_nstxout = 250
pull_nstfout = 250
pull_ngroups = 1
pull_group0  = POPC
pull_pbcatom0= 338
pull_group1  = KSC
pull_pbcatom1= 0
pull_init1   = 0 0 0.0
pull_rate1   = 0
pull_k1  = 3000.0
pull_vec1= 0 0 0
;;;EOF


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Re: [gmx-users] Timing variability


On 23/06/2011 2:32 AM, chris.ne...@utoronto.ca wrote:

Dear Users:

Has anybody else looked at simulation speed (ns/day) over the segments 
of long runs? I always benchmark and optimize my systems carefully, 
but it was only recently that I realized how much variability I am 
obtaining over long runs. Perhaps this is specific to my cluster, 
which is one reason for my post.


You can get random and large hits if someone else is sharing your 
network (yes, even Infiniband) and hitting it hard enough. You can 
sort-of diagnose this after the fact by looking at the breakdown of 
GROMACS timings and seeing where runs spend their time. diff -y -W 160 
can be useful here. Look at the MPMD flowchart in the manual (Figure 
3.15) to get an idea which parts match up with what lines.


Speak with your admins and learn what you can. You might be able to 
mitigate the effects by using fewer processors, so that your 
computation/communication ratio goes up. Your throughput is lower, but 
your efficiency is higher. Or beg for dedicated network space to see 
what quiet-conditions performance looks like.


Here is the performance (in ns/day) that I obtain with a single run. 
This is representative of what I see with 30 other runs (see list 
below). First, the distribution is bimodal, with peaks at around 80 
and 90 ns/day. Second, the values go as low as 70 ns/day (and I have 
seen as low as 50 ns/day when I look through all 30 run directories 
that differ only by the position of the umbrella restraint).


I am using gromacs 4.5.3 and I run it like this:
mpirun mdrun_mpi -deffnm md1 -dlb yes -npme 16 -cpt 30 -maxh 47 -cpi 
md1.cpt -cpo md1.cpt -px coord.xvg -pf force.xvg -noappend


I have obtained similar behaviour also with another system.

I have attempted to correlate timing with the node on which the job 
runs, the output of the ^Grid: in the .log file, the DD division of 
PME and real-space and the value of pme mesh/force, all to no avail. I 
have found one correlation whereby the very slow runs also indicate a 
high relative load for PME.


That is suggestive of network noise - PME requires global 
intra-simulation communication.


I suspect that it is some value that is being determined at run start 
time that is affecting my performance, but I am not sure what this 
could be. Perhaps the fourier-spacing is leading to different initial 
grids?


I don't think optimize_fft = yes does much any more - but you can 
verify that by inspection of the start of the log file.


Mark


Thank you (timing information and my .mdp file follows),
Chris

### Output the ns/day obtained by the run segments
$ grep Perf *log|awk '{print $4}'

78.286
82.345
81.573
83.418
92.423
90.863
85.833
91.131
91.820
71.246
76.844
91.805
92.037
85.702
92.251
89.706
88.590
89.381
90.446
81.142
76.365
76.968
76.037
79.286
79.895
79.047
78.273
79.406
78.018
78.645
78.172
80.255
81.032
81.047
77.414
78.414
80.167
79.278
80.892
82.796
81.300
77.392
71.350
73.134
76.519
75.879
80.684
81.076
87.821
90.064
88.409
80.803
88.435

### My .mdp file

constraints = all-bonds
lincs-iter =  1
lincs-order =  6
constraint_algorithm =  lincs
integrator = sd
dt = 0.004
tinit = 100
init_step=  0
nsteps = 10
nstcomm = 1
nstxout = 10
nstvout = 10
nstfout = 10
nstxtcout = 25000
nstenergy = 25000
nstlist = 5
nstlog=0 ; reduce log file size
ns_type = grid
rlist = 1
rcoulomb = 1
rvdw = 1
coulombtype = PME
ewald-rtol = 1e-5
optimize_fft = yes
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
tc_grps =  System
tau_t   =  1.0
ld_seed =  -1
ref_t = 300
gen_temp = 300
gen_vel = yes
unconstrained_start = no
gen_seed = -1
Pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 4 4
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0

; COM PULLING
pull = umbrella
pull_geometry= position
pull_dim = N N Y
pull_start   = no
pull_nstxout = 250
pull_nstfout = 250
pull_ngroups = 1
pull_group0  = POPC
pull_pbcatom0= 338
pull_group1  = KSC
pull_pbcatom1= 0
pull_init1   = 0 0 0.0
pull_rate1   = 0
pull_k1  = 3000.0
pull_vec1= 0 0 0
;;;EOF




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[gmx-users] Trajectory and ED - (not old question again)

2011-06-22 Thread Kavyashree M

Dear users,

   I did ED analysis for one of the trajectories,
when I visualised the trajectory along the first
five eigen vectors using g_nmtraj it does not
show much movements. It was a simulation of
100 ns.
My doubt is when I visualise the trajectory in
pymol calculated just after simulation I could
observe large movements in certain regions.
same regions do have movements in ED
trajectory also but not as large as this.
Why is this?

Thank you
With Regards
M. Kavyashree
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[gmx-users]Question about reduced unit for coarse grain

Dear all:
I see from the user's manual that if our input is in reduced unit,
the output will also be in reduced unit(,
ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25.  On the
contrary, if we use standard unit, the out put will be in standard unit.
This brings the question up when we use coarse grain Clementi's
model webtool (http://smog.ucsd.edu/sbm_faq.html), according to the author,
it seems that everything is in reduced unit, so the output file should also
be in reduced unit, yet I found the topology file that the energy unit is
KJ/mol. What exactly is the unit of the input and out put file? When I pull
the molecules, do I get the reduced unit result or the physical unit result?
Since I am an experimentalist, getting the physical units is more
important to me, so as to compare with the experimental results, albeit the
intrinsic difference. If I get something in reduced unit, there is necessity
for me to change it into physical unit, or at least clarify it in
comparison.
Thank you very much.

Ye
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[gmx-users] Relaxed frozen groups

2011-06-22 Thread Zack Scholl

Hi all-

Is it possible to freeze a group of atoms only partially in a
direction?  For instance, could I freeze a group inside a box of a
definite size?


Sincere thanks,

Zack
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Re: [gmx-users] Relaxed frozen groups




Zack Scholl wrote:

Hi all-

Is it possible to freeze a group of atoms only partially in a
direction?  For instance, could I freeze a group inside a box of a
definite size?




Not by defining a box, as such, but you can freeze any subset of atoms with a 
suitable index file that defines the desired freezegrps.


-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]Question about reduced unit for coarse grain

Dear all:
I see from the user's manual that if our input is in reduced unit,
the output will also be in reduced unit(,
ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25.  On the
contrary, if we use standard unit, the out put will be in standard unit.
This brings the question up when we use coarse grain Clementi's
model webtool (http://smog.ucsd.edu/sbm_faq.html), according to the author,
it seems that everything is in reduced unit, so the output file should also
be in reduced unit, yet I found the topology file that the energy unit is
KJ/mol. What exactly is the unit of the input and out put file? When I pull
the molecules, do I get the reduced unit result or the physical unit result?
Since I am an experimentalist, getting the physical units is more
important to me, so as to compare with the experimental results, albeit the
intrinsic difference. If I get something in reduced unit, there is necessity
for me to change it into physical unit, or at least clarify it in
comparison.
Thank you very much.

Ye
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Re: [gmx-users] Autocorrelation of dipole moment

2011-06-22 Thread Chathurika Abeyrathne

Thank you.
If I apply an electric field will I be able to get only positive values?


Regards,
Chathurika.




2011/6/22 André Farias de Moura mo...@ufscar.br

 sure, the ACF for a vector gives you the average cosine between that vector
 at time t=0 and the same vector at a later time lag, thus negative values
 may
 be seen as an inversion of the direction to which the vector points
 out (-1 would
 be the value for a vector lying 180 degrees away from the direction at
 t=0).

 best

 Andre

 On Tue, Jun 21, 2011 at 8:29 PM, Chathurika Abeyrathne
 c.abeyrat...@student.unimelb.edu.au wrote:
 
 
  Hi,
 
  Is it possible to get negative values for normalized autocorrelation of
  total dipole moment.
 
  Thank you.
 
 
  Regards,
  Chathurika.
 
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Re: [gmx-users]Question about reduced unit for coarse grain

2011-06-22 Thread Yang Ye

Hi,

The unit in output is in assumed to be for the standard unit input while the
value is in reduced unit.

So you need to do your own calculation to figure out what's the reduced unit
is.

Regards,
Yang Ye

On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang knightyang...@gmail.com wrote:

 Dear all:
 I see from the user's manual that if our input is in reduced unit,
 the output will also be in reduced unit(,
 ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25.  On the
 contrary, if we use standard unit, the out put will be in standard unit.
 This brings the question up when we use coarse grain Clementi's
 model webtool (http://smog.ucsd.edu/sbm_faq.html), according to the
 author, it seems that everything is in reduced unit, so the output file
 should also be in reduced unit, yet I found the topology file that the
 energy unit is KJ/mol. What exactly is the unit of the input and out put
 file? When I pull the molecules, do I get the reduced unit result or the
 physical unit result?
 Since I am an experimentalist, getting the physical units is more
 important to me, so as to compare with the experimental results, albeit the
 intrinsic difference. If I get something in reduced unit, there is necessity
 for me to change it into physical unit, or at least clarify it in
 comparison.
 Thank you very much.

 Ye

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Re: [gmx-users]Question about reduced unit for coarse grain

Hi,
Thanks for replying, Yang.
But I still did not get it fully:
1. So if we use reduced unit in input, the output and calculation is
still assumed to be in standard units? But the calculation itself is
different since the constants are different, so the result must differed a
lot. Does gromacs knows that we are using reduced unit?
2. With this program/forcefield to build top file automaticly, the
KJ/mol it gives is in the top file, so it is still part of input, in this
case , the gromacs will recognize it in the standard unit?
3. in the top file it gives:

 [ angles ]
 ;ai  aj   ak  func  th0(deg)   Ka
 1  2  3 1  0.95664E+02  0.4E+02
 2  3  4 1  0.91183E+02  0.4E+02
 3  4  5 1  0.89842E+02  0.4E+02
 4  5  6 1  0.91965E+02  0.4E+02
 5  6  7 1  0.90670E+02  0.4E+02
 6  7  8 1  0.91186E+02  0.4E+02
 7  8  9 1  0.92703E+02  0.4E+02
 8  9 10 1  0.91537E+02  0.4E+02
 9 10 11 1  0.91328E+02  0.4E+02
10 11 12 1  0.92557E+02  0.4E+02
11 12 13 1  0.93372E+02  0.4E+02
12 13 14 1  0.94347E+02  0.4E+02
13 14 15 1  0.99411E+02  0.4E+02
14 15 16 1  0.98190E+02  0.4E+02
..
 [ dihedrals ]
 ;ai  aj  ak  al  func  phi0(deg)   Kd(kJ/mol)  mult
 1  2  3  4 1  0.24358E+03  0.1E+01 1
 1  2  3  4 1  0.73074E+03  0.5E+00 3
 2  3  4  5 1  0.22823E+03  0.1E+01 1
 2  3  4  5 1  0.68469E+03  0.5E+00 3
 3  4  5  6 1  0.23172E+03  0.1E+01 1
 3  4  5  6 1  0.69515E+03  0.5E+00 3
 4  5  6  7 1  0.22982E+03  0.1E+01 1
 4  5  6  7 1  0.68946E+03  0.5E+00 3


Seems to me that this is the standard unit, yet the author of the webtool
emphasize that this structure based cg model is in reduced unit, so what
result do I got?
Has anyone used this webtool to do CG simulation and explain what is case?

Thank you all very much.

Ye

2011/6/22 Yang Ye leafyo...@yahoo.com

 Hi,

 The unit in output is in assumed to be for the standard unit input while
 the value is in reduced unit.

 So you need to do your own calculation to figure out what's the reduced
 unit is.

 Regards,
 Yang Ye

 On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang knightyang...@gmail.com wrote:

 Dear all:
 I see from the user's manual that if our input is in reduced unit,
 the output will also be in reduced unit(,
 ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25.  On the
 contrary, if we use standard unit, the out put will be in standard unit.
 This brings the question up when we use coarse grain Clementi's
 model webtool (http://smog.ucsd.edu/sbm_faq.html), according to the
 author, it seems that everything is in reduced unit, so the output file
 should also be in reduced unit, yet I found the topology file that the
 energy unit is KJ/mol. What exactly is the unit of the input and out put
 file? When I pull the molecules, do I get the reduced unit result or the
 physical unit result?
 Since I am an experimentalist, getting the physical units is more
 important to me, so as to compare with the experimental results, albeit the
 intrinsic difference. If I get something in reduced unit, there is necessity
 for me to change it into physical unit, or at least clarify it in
 comparison.
 Thank you very much.

 Ye

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[gmx-users] T-A mutation for a dimer protein

2011-06-22 Thread chris . neale


Dear Lishan:

First, it would be great to see some evidence that you have tried to  
do this yourself before posting. Your I think makes it a possible  
waste of time for us to suggest a resolution to a problem that may or  
may not exist.


Second, if indeed it is a problem, perhaps you could use two identical  
topologies with different molecule names and treat them separately.


Chris

-- original message --

Hi All,
I have a protein dimer and I want to calculate a T to A mutation free  
energy change using TI method. Since it is a dimer, it is very  
convenient (and advantageous) to mutate the T in both monomer  
simultaneously. Gromacs will write out dH/dl sum for the two mutations  
together, I think. My question is how can I change Gromacs so than  
dH/dl for T-A mutation in each monomer is written out separately?


Best,
Lishan


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Re: [gmx-users] T-A mutation for a dimer protein


On 23/06/2011 9:48 AM, yaoli...@msu.edu wrote:


Hi All,
I have a protein dimer and I want to calculate a T to A mutation free 
energy change using TI method. Since it is a dimer, it is very 
convenient (and advantageous) to mutate the T in both monomer 
simultaneously. Gromacs will write out dH/dl sum for the two mutations 
together, I think. My question is how can I change Gromacs so than 
dH/dl for T-A mutation in each monomer is written out separately?




You can't, because both have contributions from all the interactions. If 
your method is sound, i.e. both mutations can take place without 
affecting the other (big assumption IMO), surely you can just halve 
dH/dl from the combined mutation to get the single-mutation dH/dl?


Mark
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Re: [gmx-users]Question about reduced unit for coarse grain


On 23/06/2011 10:36 AM, Ye Yang wrote:

Hi,
Thanks for replying, Yang.
But I still did not get it fully:
1. So if we use reduced unit in input, the output and calculation 
is still assumed to be in standard units?


The calculation uses the same algorithm and whatever values you input. 
Nowhere have you specified that these values are in anything other than 
the standard units, so how could GROMACS know to change anything? (Nor 
can you specify such)


But the calculation itself is different since the constants are 
different, so the result must differed a lot. Does gromacs knows that 
we are using reduced unit?


No. It's up to you to use a self-consistent set of input parameters, and 
to interpret the results correctly.


2. With this program/forcefield to build top file automaticly, the 
KJ/mol it gives is in the top file, so it is still part of input, in 
this case , the gromacs will recognize it in the standard unit?


It doesn't recognize units. It follows an algorithm that is correct if 
all the quantities are measured in the standard units. If you change 
something, you have to understand all the consequences and interpret 
appropriately :-)


Mark


3. in the top file it gives:

 [ angles ]
 ;ai  aj   ak  func  th0(deg)   Ka
 1  2  3 1  0.95664E+02  0.4E+02
 2  3  4 1  0.91183E+02  0.4E+02
 3  4  5 1  0.89842E+02  0.4E+02
 4  5  6 1  0.91965E+02  0.4E+02
 5  6  7 1  0.90670E+02  0.4E+02
 6  7  8 1  0.91186E+02  0.4E+02
 7  8  9 1  0.92703E+02  0.4E+02
 8  9 10 1  0.91537E+02  0.4E+02
 9 10 11 1  0.91328E+02  0.4E+02
10 11 12 1  0.92557E+02  0.4E+02
11 12 13 1  0.93372E+02  0.4E+02
12 13 14 1  0.94347E+02  0.4E+02
13 14 15 1  0.99411E+02  0.4E+02
14 15 16 1  0.98190E+02  0.4E+02
..
 [ dihedrals ]
 ;ai  aj  ak  al  func  phi0(deg)   Kd(kJ/mol)  mult
 1  2  3  4 1  0.24358E+03  0.1E+01 1
 1  2  3  4 1  0.73074E+03  0.5E+00 3
 2  3  4  5 1  0.22823E+03  0.1E+01 1
 2  3  4  5 1  0.68469E+03  0.5E+00 3
 3  4  5  6 1  0.23172E+03  0.1E+01 1
 3  4  5  6 1  0.69515E+03  0.5E+00 3
 4  5  6  7 1  0.22982E+03  0.1E+01 1
 4  5  6  7 1  0.68946E+03  0.5E+00 3


Seems to me that this is the standard unit, yet the author of the 
webtool emphasize that this structure based cg model is in reduced 
unit, so what result do I got?

Has anyone used this webtool to do CG simulation and explain what is case?

Thank you all very much.

Ye

2011/6/22 Yang Ye leafyo...@yahoo.com mailto:leafyo...@yahoo.com

Hi,

The unit in output is in assumed to be for the standard unit input
while the value is in reduced unit.

So you need to do your own calculation to figure out what's the
reduced unit is.

Regards,
Yang Ye

On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang knightyang...@gmail.com
mailto:knightyang...@gmail.com wrote:

Dear all:
I see from the user's manual that if our input is in
reduced unit, the output will also be in reduced
unit(,ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf),
P25.  On the contrary, if we use standard unit, the out put
will be in standard unit.
This brings the question up when we use coarse grain
Clementi's model webtool (http://smog.ucsd.edu/sbm_faq.html),
according to the author, it seems that everything is in
reduced unit, so the output file should also be in reduced
unit, yet I found the topology file that the energy unit is
KJ/mol. What exactly is the unit of the input and out put
file? When I pull the molecules, do I get the reduced unit
result or the physical unit result?
Since I am an experimentalist, getting the physical
units is more important to me, so as to compare with the
experimental results, albeit the intrinsic difference. If I
get something in reduced unit, there is necessity for me to
change it into physical unit, or at least clarify it in
comparison.
Thank you very much.

Ye

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[gmx-users] Re: T-A mutation for a dimer protein

2011-06-22 Thread Lishan Yao

Dear Chris and Mark,
Thank you both for the response. I did the simulation already and Gromacs 
only gives me the total dH/dl. The two mutated sites are more than 20A alway 
from each other which makes it safe to assume that the interaction between the 
two sites is small. If I can extract dH/dl for each site, I could get a 
resonable error estimation of my calculation. Furthermore, if this is reliable 
I will do different mutations in two monomers (as long as they are away from 
each other) so that I can save my computational time by 50%. I guess this will 
involve some code change.

Best,
Lishan



 From: chris.ne...@utoronto.ca
 Subject: [gmx-users] T-A mutation for a dimer protein
 To: gmx-users@gromacs.org
 Message-ID: 20110622210442.mmbm5utlww08k...@webmail.utoronto.ca
 Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes;
 format=flowed
 
 Dear Lishan:
 
 First, it would be great to see some evidence that you have tried to  
 do this yourself before posting. Your I think makes it a possible  
 waste of time for us to suggest a resolution to a problem that may or  
 may not exist.
 
 Second, if indeed it is a problem, perhaps you could use two identical  
 topologies with different molecule names and treat them separately.
 
 Chris
 
Message: 3
Date: Thu, 23 Jun 2011 11:40:20 +1000
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] T-A mutation for a dimer protein
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4e029984.9040...@anu.edu.au
Content-Type: text/plain; charset=iso-8859-1

On 23/06/2011 9:48 AM, yaoli...@msu.edu wrote:

 Hi All,
 I have a protein dimer and I want to calculate a T to A mutation free 
 energy change using TI method. Since it is a dimer, it is very 
 convenient (and advantageous) to mutate the T in both monomer 
 simultaneously. Gromacs will write out dH/dl sum for the two mutations 
 together, I think. My question is how can I change Gromacs so than 
 dH/dl for T-A mutation in each monomer is written out separately?


You can't, because both have contributions from all the interactions. If 
your method is sound, i.e. both mutations can take place without 
affecting the other (big assumption IMO), surely you can just halve 
dH/dl from the combined mutation to get the single-mutation dH/dl?

Mark
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Re: [gmx-users]Question about reduced unit for coarse grain

Thank you very much, Mark.

Is there anyway I can know the unit of input from the top file? I am not
sure what I am getting from the webtool, although it shows kj/mol the
instruction on the web says the unit is reduced unit, which makes me
confused. In the former case I do not need to convert, but in latter case, I
need to convert to standard units. The webtool is from
http://smog.ucsd.edu/sbm_faq.html, it is developped by Dr. Onuchic's group
in UCSD.
Has anyone used this?


 [ angles ]
 ;ai  aj   ak  func  th0(deg)   Ka
 1  2  3 1  0.95664E+02  0.4E+02
 2  3  4 1  0.91183E+02  0.4E+02
 3  4  5 1  0.89842E+02  0.4E+02
 4  5  6 1  0.91965E+02  0.4E+02
 5  6  7 1  0.90670E+02  0.4E+02
 6  7  8 1  0.91186E+02  0.4E+02
 7  8  9 1  0.92703E+02  0.4E+02
 8  9 10 1  0.91537E+02  0.4E+02
 9 10 11 1  0.91328E+02  0.4E+02
10 11 12 1  0.92557E+02  0.4E+02
11 12 13 1  0.93372E+02  0.4E+02
12 13 14 1  0.94347E+02  0.4E+02
13 14 15 1  0.99411E+02  0.4E+02
14 15 16 1  0.98190E+02  0.4E+02
..
 [ dihedrals ]
 ;ai  aj  ak  al  func  phi0(deg)   Kd(kJ/mol)  mult
 1  2  3  4 1  0.24358E+03  0.1E+01 1
 1  2  3  4 1  0.73074E+03  0.5E+00 3
 2  3  4  5 1  0.22823E+03  0.1E+01 1
 2  3  4  5 1  0.68469E+03  0.5E+00 3
 3  4  5  6 1  0.23172E+03  0.1E+01 1
 3  4  5  6 1  0.69515E+03  0.5E+00 3
 4  5  6  7 1  0.22982E+03  0.1E+01 1
 4  5  6  7 1  0.68946E+03  0.5E+00 3


Thank you very much.

Ye

2011/6/22 Mark Abraham mark.abra...@anu.edu.au

 **
 On 23/06/2011 10:36 AM, Ye Yang wrote:

 Hi,
 Thanks for replying, Yang.
 But I still did not get it fully:
 1. So if we use reduced unit in input, the output and calculation is
 still assumed to be in standard units?


 The calculation uses the same algorithm and whatever values you input.
 Nowhere have you specified that these values are in anything other than the
 standard units, so how could GROMACS know to change anything? (Nor can you
 specify such)


  But the calculation itself is different since the constants are
 different, so the result must differed a lot. Does gromacs knows that we are
 using reduced unit?


 No. It's up to you to use a self-consistent set of input parameters, and to
 interpret the results correctly.


  2. With this program/forcefield to build top file automaticly, the
 KJ/mol it gives is in the top file, so it is still part of input, in this
 case , the gromacs will recognize it in the standard unit?


 It doesn't recognize units. It follows an algorithm that is correct if all
 the quantities are measured in the standard units. If you change something,
 you have to understand all the consequences and interpret appropriately :-)

 Mark


  3. in the top file it gives:

  [ angles ]
  ;ai  aj   ak  func  th0(deg)   Ka
  1  2  3 1  0.95664E+02  0.4E+02
  2  3  4 1  0.91183E+02  0.4E+02
  3  4  5 1  0.89842E+02  0.4E+02
  4  5  6 1  0.91965E+02  0.4E+02
  5  6  7 1  0.90670E+02  0.4E+02
  6  7  8 1  0.91186E+02  0.4E+02
  7  8  9 1  0.92703E+02  0.4E+02
  8  9 10 1  0.91537E+02  0.4E+02
  9 10 11 1  0.91328E+02  0.4E+02
 10 11 12 1  0.92557E+02  0.4E+02
 11 12 13 1  0.93372E+02  0.4E+02
 12 13 14 1  0.94347E+02  0.4E+02
 13 14 15 1  0.99411E+02  0.4E+02
 14 15 16 1  0.98190E+02  0.4E+02
 ..
  [ dihedrals ]
  ;ai  aj  ak  al  func  phi0(deg)   Kd(kJ/mol)  mult
  1  2  3  4 1  0.24358E+03  0.1E+01 1
  1  2  3  4 1  0.73074E+03  0.5E+00 3
  2  3  4  5 1  0.22823E+03  0.1E+01 1
  2  3  4  5 1  0.68469E+03  0.5E+00 3
  3  4  5  6 1  0.23172E+03  0.1E+01 1
  3  4  5  6 1  0.69515E+03  0.5E+00 3
  4  5  6  7 1  0.22982E+03  0.1E+01 1
  4  5  6  7 1  0.68946E+03  0.5E+00 3


 Seems to me that this is the standard unit, yet the author of the webtool
 emphasize that this structure based cg model is in reduced unit, so what
 result do I got?
 Has anyone used this webtool to do CG simulation and explain what is case?

 Thank you all very much.

 Ye

 2011/6/22 Yang Ye leafyo...@yahoo.com

 Hi,

  The unit in output is in assumed to be for the standard unit input while
 the value is in reduced unit.

  So you need to do your own calculation to figure out what's the reduced
 unit is.

  Regards,
 Yang Ye

  On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang knightyang...@gmail.comwrote:

  Dear all:

Re: [gmx-users]Question about reduced unit for coarse grain




Ye Yang wrote:

Thank you very much, Mark.

Is there anyway I can know the unit of input from the top file? I am not 
sure what I am getting from the webtool, although it shows kj/mol the 
instruction on the web says the unit is reduced unit, which makes me 
confused. In the former case I do not need to convert, but in latter 
case, I need to convert to standard units. The webtool is from 
http://smog.ucsd.edu/sbm_faq.html, it is developped by Dr. Onuchic's 
group in UCSD.

Has anyone used this?



Since this topology was not created by any standard Gromacs utility, wouldn't it 
be more efficient to contact the developers directly about implementation 
details and proper use?


-Justin

 
 [ angles ]

 ;ai  aj   ak  func  th0(deg)   Ka
 1  2  3 1  0.95664E+02  0.4E+02
 2  3  4 1  0.91183E+02  0.4E+02
 3  4  5 1  0.89842E+02  0.4E+02
 4  5  6 1  0.91965E+02  0.4E+02
 5  6  7 1  0.90670E+02  0.4E+02
 6  7  8 1  0.91186E+02  0.4E+02
 7  8  9 1  0.92703E+02  0.4E+02
 8  9 10 1  0.91537E+02  0.4E+02
 9 10 11 1  0.91328E+02  0.4E+02
10 11 12 1  0.92557E+02  0.4E+02
11 12 13 1  0.93372E+02  0.4E+02
12 13 14 1  0.94347E+02  0.4E+02
13 14 15 1  0.99411E+02  0.4E+02
14 15 16 1  0.98190E+02  0.4E+02
..
 [ dihedrals ]
 ;ai  aj  ak  al  func  phi0(deg)   Kd(kJ/mol)  mult
 1  2  3  4 1  0.24358E+03  0.1E+01 1
 1  2  3  4 1  0.73074E+03  0.5E+00 3
 2  3  4  5 1  0.22823E+03  0.1E+01 1
 2  3  4  5 1  0.68469E+03  0.5E+00 3
 3  4  5  6 1  0.23172E+03  0.1E+01 1
 3  4  5  6 1  0.69515E+03  0.5E+00 3
 4  5  6  7 1  0.22982E+03  0.1E+01 1
 4  5  6  7 1  0.68946E+03  0.5E+00 3


Thank you very much.

Ye

2011/6/22 Mark Abraham mark.abra...@anu.edu.au 
mailto:mark.abra...@anu.edu.au


__
On 23/06/2011 10:36 AM, Ye Yang wrote:

Hi,
Thanks for replying, Yang.
But I still did not get it fully:
1. So if we use reduced unit in input, the output and
calculation is still assumed to be in standard units?


The calculation uses the same algorithm and whatever values you
input. Nowhere have you specified that these values are in anything
other than the standard units, so how could GROMACS know to change
anything? (Nor can you specify such)



But the calculation itself is different since the constants are
different, so the result must differed a lot. Does gromacs knows
that we are using reduced unit?


No. It's up to you to use a self-consistent set of input parameters,
and to interpret the results correctly.



2. With this program/forcefield to build top file automaticly,
the KJ/mol it gives is in the top file, so it is still part of
input, in this case , the gromacs will recognize it in the
standard unit?


It doesn't recognize units. It follows an algorithm that is correct
if all the quantities are measured in the standard units. If you
change something, you have to understand all the consequences and
interpret appropriately :-)

Mark



3. in the top file it gives:
 
 [ angles ]

 ;ai  aj   ak  func  th0(deg)   Ka
 1  2  3 1  0.95664E+02  0.4E+02
 2  3  4 1  0.91183E+02  0.4E+02
 3  4  5 1  0.89842E+02  0.4E+02
 4  5  6 1  0.91965E+02  0.4E+02
 5  6  7 1  0.90670E+02  0.4E+02
 6  7  8 1  0.91186E+02  0.4E+02
 7  8  9 1  0.92703E+02  0.4E+02
 8  9 10 1  0.91537E+02  0.4E+02
 9 10 11 1  0.91328E+02  0.4E+02
10 11 12 1  0.92557E+02  0.4E+02
11 12 13 1  0.93372E+02  0.4E+02
12 13 14 1  0.94347E+02  0.4E+02
13 14 15 1  0.99411E+02  0.4E+02
14 15 16 1  0.98190E+02  0.4E+02
..
 [ dihedrals ]
 ;ai  aj  ak  al  func  phi0(deg)   Kd(kJ/mol)  mult
 1  2  3  4 1  0.24358E+03  0.1E+01 1
 1  2  3  4 1  0.73074E+03  0.5E+00 3
 2  3  4  5 1  0.22823E+03  0.1E+01 1
 2  3  4  5 1  0.68469E+03  0.5E+00 3
 3  4  5  6 1  0.23172E+03  0.1E+01 1
 3  4  5  6 1  0.69515E+03  0.5E+00 3
 4  5  6  7 1  0.22982E+03  0.1E+01 1
 4  5  6  7 1  0.68946E+03  0.5E+00 3


Seems to me that this is the standard unit, yet the author of the
webtool emphasize that this structure based cg model is in reduced
unit, so what result do I got?
Has anyone used this

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

2011-06-22 Thread xiaodong huang

Dear Justin and gmxers
Thank you so much for your helpful hints, but I am wondering how to check if
I have
obtained proper distributions for the desired ensemble, as suggested in
your email?
My thoughts are:
1. As for NVT ensemble, I need to check if the velocity (or speed) of
molecules in my simulation
follows a Maxwell-boltzmann distribution, and the velocity is for the
center of mass of these
molecules, not for individual atoms, right?
2. Can I also check the distribution of T in my simulation (I output T every
100 steps or so, and
make a statistics)? It is said in NVT ensemble, T follows a gaussian
distribution, according
to central limit theorem, and the square of its variance is 2T*T/(3N). Is
that correct?
3. As for NPT ensemble, how to check if I have get a correction distribution
from pressure
coupling? Can I also check the P or V distribution? If so, what is the
correct distribution I
should get? I find some clues at Understanding Modern Molecular
Dynamics
J. Phys. Chem. B 2000, 104, 159-178, but this paper just discuss some
simple systems
in T,P coupling section, and I still do not know the correct distribution
I should
get for my own simulations (e.g. protein in a box of water, NPT).
4.Are there any other quantities I need to check to make sure I have sampled
a correct
ensemble? I think to check the distribution of v, T, P V should be enough
for this purpose,
lthough to check more quantities is a plus, right?
Any suggestions or comments are very welcome. Thank you.
yours
xiaodong
Research School of Chemistry
ANU

On Tue, Jun 21, 2011 at 11:21 PM, Justin A. Lemkul jalem...@vt.edu wrote:

xiaodong huang wrote:

Dear gromacs-ers

I am using stochastic dynamics integrator (integrator = sd), so most of
the time, I only need to adjust following parameters for temperature and
pressure coupling: tau_t pcoupl tau_p (ref_t is room temperature and ref_p
is 1 atm, compressibility can be taken from experimental numbers).

In the manual, a tau_t between 1 and 2ps is recommended for the sake of
simulation stability, but I see someone use a tau_t of 0.1ps with the same
integrator (integration was performed with Langevin dynamics,49 with a
reference temperature of 300 K and a weak frictional constant of 10 ps-1,)
when simulating water solvent. I also see someone use a tau_t of 0.2ps with
the same integrator (To obtain a isothermal–isobaric ensemble at 293 K, a
leap-frog stochastic dynamics integrator16 was used to integrate the
equations of motion. The inverse friction constant was set to 0.2 ps.) when
simulating some organic solvent. I check the references mentioned in these
gromacs papers so I am pretty sure they are using the same integrator. So I
am a bit confusing here, what tau_t should I use, the number between 1 and
2ps as recommended by the manual, or the numbers below 1ps, as reported in
these papers? Does this parameter depend on what solvent (water,
cyclohexane) I use? Can I just use any number between 0.1ps and 2ps and
check if my simulations look fine or there is some ‘best’ number for a
particular solvent?

This was discussed recently:

http://lists.gromacs.org/**pipermail/gmx-users/2011-June/**061992.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html

When I use berendsen or Parrinello-Rahman, the same questions apply: Is
there some ‘best’ number for a particular solvent, or I can just use any
number between 0.5ps and 5ps and check if my simulations run well?

When I read papers, I find many different pressure coupling constant
(tau_p) ranging from 0.5ps to 1ps (water), 1ps to 5ps (organic solvent) with
weak coupling scheme in gromacs. I am wondering why they use bigger number
for organic solvent? If I use Parrinello-Rahman (it is said to be better
than berendsen in the manual), do I need to change tau_p, or I can just use
the same tau_p as berendsen?

Time constants are a bit empirical. The Berendsen algorithm is more
forgiving; it relaxes very quickly and thus low values of tau_t/tau_p are
stable. For methods that allow for wider oscillations (N-H for temperature,
P-R for pressure), small tau_t/tau_p values are unstable due to the nature
of these algorithms. The most important information is whether or not you
obtain proper distributions for the desired ensemble. Any algorithm can be
made to behave artificially rigorously or artificially relaxed.

-Justin

Thank you so much for your kind help, any suggestions or clues are very
welcome.

Yours

xiaodong huang
Research School of Chemistry
ANU

--
==**==

==**==
--

RE: [gmx-users] Fw: properdihedrals

2011-06-22 Thread Emanuel Birru

Could you clarify your question??

Do you want to change the default dihedrals of Gromacs to RB dihedral potential 
and to Furiour function? If so check the Gromacs manual for 4.5, pages 72-74.

Cheers,
Emanuel






=
Emanuel Birru
PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187
E-mail: emanuel.bi...@monash.edumailto:firstname.lastn...@monash.edu
www.pharm.monash.edu.auhttp://www.pharm.monash.edu.au

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Prema Awati
Sent: Wednesday, 22 June 2011 4:05 AM
To: gmx-users@gromacs.org
Cc: vvcha...@gmail.com
Subject: [gmx-users] Fw: properdihedrals



-- Original Message --
From: prem...@iiserpune.ac.in
To: gmxus...@gromacs.org
Date: Tue, 21 Jun 2011 23:25:51 +0530 (GMT+05:30)
Subject: properdihedrals

Sir,
I am looking forward for your help to calculate Ryckaert-Belleman's (RB) 
coefficients using proper dihedrals.Is there any way to get Fourier 
coefficients value from the equation;
Vd (φijkl ) = kφ (1 + cos(nφ − φs )) ; so that I can use it in following way to 
get RB coefficients;

C0 = F2 + 1 (F1 + F3 )
C1 = 1 (−F1 + 3 F3 )
C2 = −F2 + 4 F4
C3 = −2 F3
C4 = −4 F4
C5 = 0
I am referring Gromacs-4.5.3 manual for the above conversion.
Looking for your quick response
Thankyou.


-- 
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Re: [gmx-users] Re: T-A mutation for a dimer protein


On 23/06/2011 12:22 PM, Lishan Yao wrote:

Dear Chris and Mark,
 Thank you both for the response. I did the simulation already and Gromacs 
only gives me the total dH/dl.


So what's wrong with dividing by two, like I suggested last time? You've 
got two events and you assert that they're independent, so the 
statistics should be easy.



  The two mutated sites are more than 20A alway from each other which makes it 
safe to assume that the interaction between the two sites is small. If I can 
extract dH/dl for each site, I could get a resonable error estimation of my 
calculation. Furthermore, if this is reliable I will do different mutations in 
two monomers (as long as they are away from each other) so that I can save my 
computational time by 50%. I guess this will involve some code change.


To which mutation would you assign the energy contribution of the atoms 
around half way between them?


Mark


Best,
Lishan




From: chris.ne...@utoronto.ca
Subject: [gmx-users] T-A mutation for a dimer protein
To: gmx-users@gromacs.org
Message-ID:20110622210442.mmbm5utlww08k...@webmail.utoronto.ca
Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes;
format=flowed

Dear Lishan:

First, it would be great to see some evidence that you have tried to
do this yourself before posting. Your I think makes it a possible
waste of time for us to suggest a resolution to a problem that may or
may not exist.

Second, if indeed it is a problem, perhaps you could use two identical
topologies with different molecule names and treat them separately.

Chris


Message: 3
Date: Thu, 23 Jun 2011 11:40:20 +1000
From: Mark Abrahammark.abra...@anu.edu.au
Subject: Re: [gmx-users] T-A mutation for a dimer protein
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Message-ID:4e029984.9040...@anu.edu.au
Content-Type: text/plain; charset=iso-8859-1

On 23/06/2011 9:48 AM, yaoli...@msu.edu wrote:

Hi All,
I have a protein dimer and I want to calculate a T to A mutation free
energy change using TI method. Since it is a dimer, it is very
convenient (and advantageous) to mutate the T in both monomer
simultaneously. Gromacs will write out dH/dl sum for the two mutations
together, I think. My question is how can I change Gromacs so than
dH/dl for T-A mutation in each monomer is written out separately?


You can't, because both have contributions from all the interactions. If
your method is sound, i.e. both mutations can take place without
affecting the other (big assumption IMO), surely you can just halve
dH/dl from the combined mutation to get the single-mutation dH/dl?

Mark


--
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Please search the archive at 
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Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?


On 23/06/2011 12:38 PM, xiaodong huang wrote:

Dear Justin and gmxers
Thank you so much for your helpful hints, but I am wondering how to 
check if I have
obtained proper distributions for the desired ensemble, as suggested 
in your email?

My thoughts are:
1. As for NVT ensemble, I need to check if the velocity (or speed) of 
molecules in my simulation
follows a Maxwell-boltzmann distribution, and the velocity is for 
the center of mass of these

molecules, not for individual atoms, right?


Atoms are physical. Molecules are a convenient grouping of them to aid 
human understanding.


2. Can I also check the distribution of T in my simulation (I output T 
every 100 steps or so, and
make a statistics)? It is said in NVT ensemble, T follows a 
gaussian distribution, according
   to central limit theorem, and the square of its variance is 
2T*T/(3N). Is that correct?


g_energy will report some descriptive statistics.

3. As for NPT ensemble, how to check if I have get a correction 
distribution from pressure
coupling? Can I also check the P or V distribution? If so, what is 
the correct distribution I
should get? I find some clues at Understanding Modern Molecular 
Dynamics
   J. Phys. Chem. B 2000, 104, 159-178, but this paper just discuss 
some simple systems
   in T,P coupling section, and I still do not know the correct 
distribution I should

   get for my own simulations (e.g. protein in a box of water, NPT).


You need to use a small system that you can exhaustively sample, deduce 
what the statistical distribution of your observables should be, and see 
what you get. Or you can simply rely on the use of algorithms that have 
been shown to produce correct distributions, and trust/verify that 
GROMACS has implemented them correctly.


Mark

4.Are there any other quantities I need to check to make sure I have 
sampled a correct
   ensemble? I think to check the distribution of v, T, P V should be 
enough for this purpose,

   lthough to check more quantities is a plus, right?
Any suggestions or comments are very welcome. Thank you.
yours
xiaodong
Research School of Chemistry
ANU

On Tue, Jun 21, 2011 at 11:21 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




xiaodong huang wrote:

Dear gromacs-ers

I am using stochastic dynamics integrator (integrator = sd),
so most of the time, I only need to adjust following
parameters for temperature and pressure coupling: tau_t pcoupl
tau_p (ref_t is room temperature and ref_p is 1 atm,
compressibility can be taken from experimental numbers).


In the manual, a tau_t between 1 and 2ps is recommended for
the sake of simulation stability, but I see someone use a
tau_t of 0.1ps with the same integrator (integration was
performed with Langevin dynamics,49 with a reference
temperature of 300 K and a weak frictional constant of 10
ps-1,) when simulating water solvent. I also see someone use a
tau_t of 0.2ps with the same integrator (To obtain a
isothermal–isobaric ensemble at 293 K, a leap-frog stochastic
dynamics integrator16 was used to integrate the equations of
motion. The inverse friction constant was set to 0.2 ps.) when
simulating some organic solvent. I check the references
mentioned in these gromacs papers so I am pretty sure they are
using the same integrator. So I am a bit confusing here, what
tau_t should I use, the number between 1 and 2ps as
recommended by the manual, or the numbers below 1ps, as
reported in these papers? Does this parameter depend on what
solvent (water, cyclohexane) I use? Can I just use any number
between 0.1ps and 2ps and check if my simulations look fine or
there is some ‘best’ number for a particular solvent?


This was discussed recently:

http://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html



When I use berendsen or Parrinello-Rahman, the same questions
apply: Is there some ‘best’ number for a particular solvent,
or I can just use any number between 0.5ps and 5ps and check
if my simulations run well?


When I read papers, I find many different pressure coupling
constant (tau_p) ranging from 0.5ps to 1ps (water), 1ps to 5ps
(organic solvent) with weak coupling scheme in gromacs. I am
wondering why they use bigger number for organic solvent? If I
use Parrinello-Rahman (it is said to be better than berendsen
in the manual), do I need to change tau_p, or I can just use
the same tau_p as berendsen?


Time constants are a bit empirical.  The Berendsen algorithm is
more forgiving; it relaxes very quickly and thus low values of
tau_t/tau_p are stable.  For methods that allow for wider
oscillations (N-H for temperature, P-R for pressure), small
tau_t/tau_p values are

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?




xiaodong huang wrote:

Dear Justin and gmxers
Thank you so much for your helpful hints, but I am wondering how to 
check if I have
obtained proper distributions for the desired ensemble, as suggested 
in your email?

My thoughts are:
1. As for NVT ensemble, I need to check if the velocity (or speed) of 
molecules in my simulation
follows a Maxwell-boltzmann distribution, and the velocity is for 
the center of mass of these

molecules, not for individual atoms, right?


Ideally, you'd get this distribution for a simple system, but the actual 
distribution will be determined by how well the thermostatting algorithm 
actually reproduces the expected behavior.  You would have to consider 
molecules, especially if you've used constraints.


2. Can I also check the distribution of T in my simulation (I output T 
every 100 steps or so, and
make a statistics)? It is said in NVT ensemble, T follows a gaussian 
distribution, according
   to central limit theorem, and the square of its variance is 
2T*T/(3N). Is that correct?


g_energy will report all of these statistics; you do not need to assemble them 
manually.  Again, the distribution is only as good as the thermostatting algorithm.


3. As for NPT ensemble, how to check if I have get a correction 
distribution from pressure
coupling? Can I also check the P or V distribution? If so, what is 
the correct distribution I
should get? I find some clues at Understanding Modern Molecular 
Dynamics
   J. Phys. Chem. B 2000, 104, 159-178, but this paper just discuss 
some simple systems
   in T,P coupling section, and I still do not know the correct 
distribution I should

   get for my own simulations (e.g. protein in a box of water, NPT).


Read about your chosen barostat and how it is generally applied to such systems. 
 This will tell you what type of distribution might be expected.  Pressure 
values oscillate wildly in a simulation.  Do not expect to get any sort of nice 
distribution from them :)


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

4.Are there any other quantities I need to check to make sure I have 
sampled a correct
   ensemble? I think to check the distribution of v, T, P V should be 
enough for this purpose,

   lthough to check more quantities is a plus, right?


For an NPT ensemble, achieving the desired T and P (since v and T are not 
independent, just as P and V are not) is the first step.  As I've said, the 
distributions depend on the algorithms and how faithfully they reproduce reality.


-Justin


Any suggestions or comments are very welcome. Thank you.
yours
xiaodong
Research School of Chemistry
ANU

On Tue, Jun 21, 2011 at 11:21 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




xiaodong huang wrote:

Dear gromacs-ers

I am using stochastic dynamics integrator (integrator = sd), so
most of the time, I only need to adjust following parameters for
temperature and pressure coupling: tau_t pcoupl tau_p (ref_t is
room temperature and ref_p is 1 atm, compressibility can be
taken from experimental numbers).

 
In the manual, a tau_t between 1 and 2ps is recommended for the

sake of simulation stability, but I see someone use a tau_t of
0.1ps with the same integrator (integration was performed with
Langevin dynamics,49 with a reference temperature of 300 K and a
weak frictional constant of 10 ps-1,) when simulating water
solvent. I also see someone use a tau_t of 0.2ps with the same
integrator (To obtain a isothermal–isobaric ensemble at 293 K, a
leap-frog stochastic dynamics integrator16 was used to integrate
the equations of motion. The inverse friction constant was set
to 0.2 ps.) when simulating some organic solvent. I check the
references mentioned in these gromacs papers so I am pretty sure
they are using the same integrator. So I am a bit confusing
here, what tau_t should I use, the number between 1 and 2ps as
recommended by the manual, or the numbers below 1ps, as reported
in these papers? Does this parameter depend on what solvent
(water, cyclohexane) I use? Can I just use any number between
0.1ps and 2ps and check if my simulations look fine or there is
some ‘best’ number for a particular solvent?


This was discussed recently:

http://lists.gromacs.org/__pipermail/gmx-users/2011-June/__061992.html
http://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html


 
When I use berendsen or Parrinello-Rahman, the same questions

apply: Is there some ‘best’ number for a particular solvent, or
I can just use any number between 0.5ps and 5ps and check if my
simulations run well?

 
When I read papers, I find many different pressure coupling

constant (tau_p) ranging from 0.5ps to 1ps (water), 1ps to 5ps

Re: [gmx-users]Question about reduced unit for coarse grain




Ye Yang wrote:

 Just no reply from them for some time...


Well, that's unfortunate.  I'd hazard a guess that all the units are reduced, 
but that's just a hunch.  Theoretically, all your input and output should be in 
reduced units.  My hunch is based on the fact that everything shown (in terms of 
force constants) is a nice, round number (5, 10, 400) which seems odd for 
standard values (see any ffbonded.itp for normal values).  It looks like 
everything is relative to the reduced units, but to be sure you'd really have to 
get a response from those who developed the web service you're trying to use, if 
this information is not otherwise documented somewhere (FAQ's, publication, etc).


-Justin


Thank you anyway.

Ye
2011/6/22 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu



Ye Yang wrote:

Thank you very much, Mark.

Is there anyway I can know the unit of input from the top file?
I am not sure what I am getting from the webtool, although it
shows kj/mol the instruction on the web says the unit is
reduced unit, which makes me confused. In the former case I do
not need to convert, but in latter case, I need to convert to
standard units. The webtool is from
http://smog.ucsd.edu/sbm_faq.__html
http://smog.ucsd.edu/sbm_faq.html, it is developped by Dr.
Onuchic's group in UCSD.
Has anyone used this?


Since this topology was not created by any standard Gromacs utility,
wouldn't it be more efficient to contact the developers directly
about implementation details and proper use?

-Justin

 [ angles ]
 ;ai  aj   ak  func  th0(deg)   Ka
1  2  3 1  0.95664E+02  0.4E+02
2  3  4 1  0.91183E+02  0.4E+02
3  4  5 1  0.89842E+02  0.4E+02
4  5  6 1  0.91965E+02  0.4E+02
5  6  7 1  0.90670E+02  0.4E+02
6  7  8 1  0.91186E+02  0.4E+02
7  8  9 1  0.92703E+02  0.4E+02
8  9 10 1  0.91537E+02  0.4E+02
9 10 11 1  0.91328E+02  0.4E+02
   10 11 12 1  0.92557E+02  0.4E+02
   11 12 13 1  0.93372E+02  0.4E+02
   12 13 14 1  0.94347E+02  0.4E+02
   13 14 15 1  0.99411E+02  0.4E+02
   14 15 16 1  0.98190E+02  0.4E+02
..
 [ dihedrals ]
 ;ai  aj  ak  al  func  phi0(deg)   Kd(kJ/mol)  mult
1  2  3  4 1  0.24358E+03  0.1E+01 1
1  2  3  4 1  0.73074E+03  0.5E+00 3
2  3  4  5 1  0.22823E+03  0.1E+01 1
2  3  4  5 1  0.68469E+03  0.5E+00 3
3  4  5  6 1  0.23172E+03  0.1E+01 1
3  4  5  6 1  0.69515E+03  0.5E+00 3
4  5  6  7 1  0.22982E+03  0.1E+01 1
4  5  6  7 1  0.68946E+03  0.5E+00 3


Thank you very much.

Ye

2011/6/22 Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.__au mailto:mark.abra...@anu.edu.au


   __
   On 23/06/2011 10:36 AM, Ye Yang wrote:

   Hi,
   Thanks for replying, Yang.
   But I still did not get it fully:
   1. So if we use reduced unit in input, the output and
   calculation is still assumed to be in standard units?


   The calculation uses the same algorithm and whatever values you
   input. Nowhere have you specified that these values are in
anything
   other than the standard units, so how could GROMACS know to
change
   anything? (Nor can you specify such)


   But the calculation itself is different since the
constants are
   different, so the result must differed a lot. Does
gromacs knows
   that we are using reduced unit?


   No. It's up to you to use a self-consistent set of input
parameters,
   and to interpret the results correctly.


   2. With this program/forcefield to build top file
automaticly,
   the KJ/mol it gives is in the top file, so it is still
part of
   input, in this case , the gromacs will recognize it in the
   standard unit?


   It doesn't recognize units. It follows an algorithm that is
correct
   if all the quantities are measured in the standard units. If you
   change something, you have to understand all the consequences and
   interpret appropriately :-)

   Mark


   3. in the top file it gives:
 [ angles ]
;ai

Re: [gmx-users]Question about reduced unit for coarse grain