Re: [gmx-users] Free energy of discharging and then recharging not zero

[Maik Goette]

Hi Robert

I wouldn't expect that either. Morphing G to A should yield quite 
reasonable results, cause you just have few dummies in your system.

The process, you describe is the way, one would think of, yes.
Just to get you right. Are you swithing off charges of a whole base or 
nucleotide? In the case of a nucleotide, you morph away one netto 
charge. That could be problematic with PME (?). Maybe trying reaction 
field could help here.


Now, if you turn off the charges of the base and then turn it on again, 
both contributions should actually lead to the same values, as David said.
As long, as no dummies are involved, everything should run smooth. I 
suggest, you simply do position restrained simulations at the discrete 
lambda steps, when turning on/off your charges. Maybe, they converge 
faster then. This would indicate a sampling problem, indeed.


For a purine to pyrimidine morph (or vice versa), I'm still convinced, 
that you would have to sample for ages to get a converged system, though.


Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Robert Johnson wrote:

Hi Maik,
That's exactly what I'm attempting to do...morph G to A etc. All I'm
doing here is turning off the charges of G and then turning them on
again. Wouldn't you do this anyway in the morph step? Wouldn't the
process go something like: Turn off charges -> Morph LJ parameters ->
Turn on charges.

It seems like I've got to be doing something wrong. I can't believe
that simply turning off/on the charges would drastically perturb the
entire system and prevent convergence.
Bob


On Thu, May 8, 2008 at 6:12 AM, Maik Goette <[EMAIL PROTECTED]> wrote:

Hi Robert

 Sounds familiar to me. I also tried to compute free energy differences by
letting whole bases appear/disappear. I ran into the same problems and
haven't found a solution yet. Probably the perturbation is too large to gain
converged results. My solution was stopping those simulations.
 This doesn't sound promising, I know, but actually, I fear, there is no
proper solution. Maybe you should morph G to A or T to C or something like
that, where just a few atoms have to be perturbed.

 Regards

 Maik Goette, Dipl. Biol.
 Max Planck Institute for Biophysical Chemistry
 Theoretical & computational biophysics department
 Am Fassberg 11
 37077 Goettingen
 Germany
 Tel.  : ++49 551 201 2310
 Fax   : ++49 551 201 2302
 Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
 WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


 Robert Johnson wrote:




Hello everyone,
I'm trying to calculate the free energy of binding of DNA bases on a
carbon nanotube. I'm running some tests to make sure that I'm doing
everything correctly. One thing I tried was turning off all the atom
charges of the DNA base and then turning them back on again.
Theoretically, the free energy changes of these two processes should
be equal and opposite and thus sum to zero. However, this is not what
I'm finding.

For guanine, I get a free energy change of 648 kJ/mol and -618 kJ/mol
for turning off and turning on the charges, respectively. Obviously,
they are not equal by 30 kJ/mol, which seems pretty big. I have done
some error estimation using the g_analyze -ee program. One thing I
find strange is that the error estimates in dV/dl for TURNING ON the
charges is large (over 2) and do not even converge for a 7.5 ns
simulation. In contrast, the error in dV/dl for TURNING OFF the
charges converges extremely quickly (using small block sizes of 50 or
less) and is smaller at 0.3. So it seems like I have some sampling
problems with the TURNING ON portion. Is there some reason why you
must sample a longer trajectory when turning on the charges?

I'm following the procedures of
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial

Does anyone know the reason for the discrepancy between these two
(seemingly identical) processes?

Thanks,
Bob

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[gmx-users] QM/MM compilation

[Ramon Crehuet]

Dear all,
I would like to install the QM/MM support for gromacs 3.3. According to
the wiki page I should follow the instructions in:
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/qmmm.html
where it says that:
"From version 3.3 onwards, the default gromacs distributions support QM/MM."
I assume that I need to compile gromacs configuring --with-qmmm-mopac and
then do I need libmopac.a as well? Where should I put it?
Is there any document with detailed information on the compilation process?

Besides, I am especially interested in using the newer Mopac2007. Is that
possible with gromacs? Could someone please tell me how to proceed?
Thanks in advance,
Ramon
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[gmx-users] chirality check

[sanjay23]

dear gromacs user,
i am doing simlation of a small molecules which have chiral corbon. i want
to chechk whethere the chirality maintaned during simulation or not, any
one sugest me how to check it.
thanks
sanjay

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Re: [gmx-users] [ angle_restraints_z ]

[Terry Nelson]

Dear Berk,

Thanks for the reply.

Yes. In fact I made the choice of multiplicity=1 based on  the explanation
in eq. 4.68:

"A multiplicity (n) of 2 is useful when you do not want to distinguish
between parallel and anti-parallel vectors."

Since my molecule is slightly polar and it may matter whether it is at 0 or
180 orientation, I decided to use multiplicity of 1.

Please correct me if I am missing something.

If multiplicity 1 is OK do you still think that the force constant 1000
kJ/mo is too large in my system?


On Mon, May 19, 2008 at 5:34 PM, Berk Hess <[EMAIL PROTECTED]> wrote:

>
>
>
>
> --
> Date: Sat, 17 May 2008 08:48:28 +0330
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] [ angle_restraints_z ]
>
>
> Hi all,
>
> There are atoms (a1 and a2) in my small molecule coordinate file  that have
> the same z component:
> a1: atom#22 (x1,y1,60.231)
> a2: atom#45 (x2,y2,60.231)If I use these lines only
>
> Therefore the vector a1-a2 makes theta=90o with the z-axis.  in my previous
> MD runs the a1-a2 were flexible (theta was observed in the range of 30-120
> degrees).
> To restrain a1-a2 at this orientation throughout my MD calculations I
> included these lines to my starting topology:
>
> ; Restrain the molecules wrt z-axis...
> [ angle_restraints_z ]
> ; #1 #2  typetheta0(degrees)  k_c(kJ mpl^(-1))  multiplicity
> 22  45 1   90 10001
>
> Would someone comment on:
> - Is this is all I need to do to restrain a1-12 wrt z-axis?
> - Are the above parameters (theta/K/multiplicity) reasonable/correct?
> - with this I should expect a1 and a2 stay in xy-plane (with their z
> component equal at each frame) during minimization, equilibration and
> production?
>
> Thanks.
>
> --
> Cheers,
> Terry
>
>
> Did you look at formula 4.68 in the manual?
> What you want is a minimum at 90 and maxima at 0 and 180.
> So you need to use a multiplicity of 2.
> 1000 as a force constant seems too large to me, this means that
> the 0/180 degrees is penalized by 2000 kJ/mol.
>
> Berk.
>
>
> --
> Express yourself instantly with MSN Messenger! MSN 
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-- 
Cheers,
Terry
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RE: [gmx-users] [ angle_restraints_z ]

[Berk Hess]

Hi,

I think you do not want to distinguish between parallel and anti-parallel.
But in your case using multiplicity 1 or 2 does not matter much.
1000 kJ/mol makes the orientation extremely rigid, but I don't know
how rigid you want to have it.
100 kJ/mol is probably a more reasonable order of magnitude.

Berk


Date: Tue, 20 May 2008 16:39:22 +0430
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] [ angle_restraints_z ]

Dear Berk,

Thanks for the reply.
 
Yes. In fact I made the choice of multiplicity=1 based on  the explanation in 
eq. 4.68:

"A multiplicity (n) of 2 is useful when you do not want to distinguish between 
parallel and anti-parallel vectors."


Since my molecule is slightly polar and it may matter whether it is at 0 or 180 
orientation, I decided to use multiplicity of 1. 

Please correct me if I am missing something.

If multiplicity 1 is OK do you still think that the force constant 1000 kJ/mo 
is too large in my system?



On Mon, May 19, 2008 at 5:34 PM, Berk Hess <[EMAIL PROTECTED]> wrote:









Date: Sat, 17 May 2008 08:48:28 +0330
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org

Subject: [gmx-users] [ angle_restraints_z ]

Hi all,


There are atoms (a1 and a2) in my small molecule coordinate file  that have the 
same z component:

a1: atom#22 (x1,y1,60.231)

a2: atom#45 (x2,y2,60.231)If I use these lines only



Therefore the vector a1-a2 makes theta=90o with the z-axis.  in my
previous MD runs the a1-a2 were flexible (theta was observed in the
range of 30-120 degrees). 

To restrain a1-a2 at this orientation throughout my MD calculations I included 
these lines to my starting topology:



; Restrain the molecules wrt z-axis...

[ angle_restraints_z ]

; #1 #2  typetheta0(degrees)  k_c(kJ mpl^(-1))  multiplicity

22  45 1   90 10001



Would someone comment on:

- Is this is all I need to do to restrain a1-12 wrt z-axis?

- Are the above parameters (theta/K/multiplicity) reasonable/correct?

- with this I should expect a1 and a2 stay in xy-plane (with their z
component equal at each frame) during minimization, equilibration and
production?



Thanks.
-- 
Cheers,
Terry

Did you look at formula 4.68 in the manual?
What you want is a minimum at 90 and maxima at 0 and 180.
So you need to use a multiplicity of 2.

1000 as a force constant seems too large to me, this means that
the 0/180 degrees is penalized by 2000 kJ/mol.

Berk.



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-- 
Cheers,
Terry

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Re: [gmx-users] chirality check

[Daniel Larsson]

DIY solution:

You can calculate the location of the carbon relatively to a plane  
defined by three of the atoms bound to the carbon. To be on the safe  
side, also calculate on which side the fourth atom is located (should  
be the same as the carbon).


- Daniel


On May 20, 2008, at 13:19, [EMAIL PROTECTED] wrote:


dear gromacs user,
i am doing simlation of a small molecules which have chiral corbon.  
i want
to chechk whethere the chirality maintaned during simulation or  
not, any

one sugest me how to check it.
thanks
sanjay

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---

Daniel Larsson
Molecular Biophysics group
Department of Cell and Molecular Biology
Uppsala University

+46-18-471 4006 (phone)
+46-18-511 755  (fax)
http://xray.bmc.uu.se/~larsson
[EMAIL PROTECTED]



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Re: [gmx-users] Free energy calculations and speed problems

[Justin A. Lemkul]

Just to follow up - the cutoff scheme worked quite well.  It gave me energies
that were ~1% different from those of the PME calculation, which I think
compares quite well.  The 10-ps run I attempted now takes 3 seconds, instead of
20 minutes.

Thanks to everyone for the suggestions.

-Justin

Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:

>
> Thanks to everyone for the insights.  I'll try running things with the cutoff
> and see how it goes.
>
> -Justin
>
> Quoting Michael Shirts <[EMAIL PROTECTED]>:
>
> > Hi, Justin-
> >
> > Have you considered -not- running PME in vacuo?  If you set your
> > cutoffs and rlist large enough, then you can just run with simple
> > cutoffs, and it should run -fst-.  Of course, you should compare
> > to the energy with PME -- if they are not equivalent, then you many
> > need to go back and check your PME parameters for accuracy.
> >
> > Best,
> > Michael
> >
> > > I'm running some free energy calculations (in vacuo and in solution) for
> a
> > set
> > > of molecules I am trying to parameterize.  All the molecules are fairly
> > small,
> > > about 30-35 atoms in each.  The solvated calculations go smoothly, and
> > rather
> > > quickly (~5 hr/ns on two nodes).  I am running into a problem when I do
> the
> > in
> > > vacuo calculations.  Since I am constraining all bonds, I am running
> things
> > on
> > > a local machine in the lab (single core AMD64 Opteron).  I get as far as
> > NVT
> > > equilibration (removing charges only) before I give up and kill it, since
> > it
> > > takes so long.  A 10-ps NVT run takes about 20 minutes, but that adds up
> to
> > > over 5 days for my 5-ns production run!  The machine is no slouch; I have
> > used
> > > it to run other small NVT/NPT/MD runs with good performance.  I get
> similar
> > > performance on another machine that is even faster (a single CPU of the
> > 2-CPU
> > > node on our supercomputer).  The installations of Gromacs on both are
> fine,
> > as
> > > far as I can tell, and both have been used extensively.
> > >
> > > I am using Gromacs version 3.3.3, and I have attached my .mdp file and
> the
> > tail
> > > end of my log file for reference.  If anyone notices anything obvious
> that
> > I'm
> > > doing wrong, I would be grateful if you pointed it out!  I see in the log
> > of
> > > the slow run (in vacuo) that the 3D-FFT calculation is dominating the CPU
> > > usage.  Is that indicative of any problem?
> > >
> > > Thanks for your attention.
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> >
>
>
>
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> 
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>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] QM/MM compilation

[ggroenh]

--

Message: 1
Date: Tue, 20 May 2008 12:52:41 +0200
From: "Ramon Crehuet" <[EMAIL PROTECTED]>
Subject: [gmx-users] QM/MM compilation
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"

Dear all,
I would like to install the QM/MM support for gromacs 3.3. According  
to

the wiki page I should follow the instructions in:
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/qmmm.html
where it says that:
"From version 3.3 onwards, the default gromacs distributions support  
QM/MM."
I assume that I need to compile gromacs configuring --with-qmmm- 
mopac and

then do I need libmopac.a as well? Where should I put it?
Is there any document with detailed information on the compilation  
process?


Configure with

--with-qmmm-gaussian
--with-qmmm-gamess

or

--with-qmmm-mopac

for qm/mm with the respective packages.
Mopac2007 is not supported, only mopac7, the last release of the  
public domain version.
You need to compile all sources, link them up in a library, and use  
the LDFLAGS and LIBS to let the configure script know where to find  
the libraries.


We have experimented with ifort and f2c/gcc to compile mopac. Reliable  
results were obtained only with f2c and a 32 bit gcc compiler.



Hope this helps,


Gerrit







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Re: [gmx-users] QM/MM compilation

[Ran Friedman]

Dear Gerrit,

Hitch-hiking with a related issue. I  saw on your presentation for the
Stanford workshop that GMX can work with DFTB. Is this just planned?

Ran.

ggroenh wrote:
>> --
>>
>> Message: 1
>> Date: Tue, 20 May 2008 12:52:41 +0200
>> From: "Ramon Crehuet" <[EMAIL PROTECTED]>
>> Subject: [gmx-users] QM/MM compilation
>> To: gmx-users@gromacs.org
>> Message-ID:
>> <[EMAIL PROTECTED]>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Dear all,
>> I would like to install the QM/MM support for gromacs 3.3. According to
>> the wiki page I should follow the instructions in:
>> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/qmmm.html
>>
>> where it says that:
>> "From version 3.3 onwards, the default gromacs distributions support
>> QM/MM."
>> I assume that I need to compile gromacs configuring --with-qmmm-mopac
>> and
>> then do I need libmopac.a as well? Where should I put it?
>> Is there any document with detailed information on the compilation
>> process?
>
> Configure with
>
> --with-qmmm-gaussian
> --with-qmmm-gamess
>
> or
>
> --with-qmmm-mopac
>
> for qm/mm with the respective packages.
> Mopac2007 is not supported, only mopac7, the last release of the
> public domain version.
> You need to compile all sources, link them up in a library, and use
> the LDFLAGS and LIBS to let the configure script know where to find
> the libraries.
>
> We have experimented with ifort and f2c/gcc to compile mopac. Reliable
> results were obtained only with f2c and a 32 bit gcc compiler.
>
>
> Hope this helps,
>
>
> Gerrit
>

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Re: [gmx-users] Free energy calculations and speed problems

[David Mobley]

Justin and Michael,

Just to clarify here, I don't think you want the "long cutoff in
vacuum" scheme to give you the same results as the "PME in vacuum"
scheme. That is, if you use PME in vacuum with a periodic box, you
will be including copies of the long-range unscreened electrostatic
interactions between your molecule and its periodic copies. Unless
your box is gigantic, you will probably see significant contributions
to the energy from these. I think for most ordinary vacuum
calculations (i.e. comparing to a vacuum reference state for, say,
hydration free energies) you don't want these contributions and your
desired reference state is something more like the molecule in vacuum,
with no cutoffs, but with no periodic copies. You can achieve that
most easily by simply running in vacuum without pme but making the
cutoffs huge enough to include all of the intramolecular interactions.
Of course, for a protein this would probably be a bad idea for speed
reasons, but for small molecules it can work well.

David


On Tue, May 20, 2008 at 8:06 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
> Just to follow up - the cutoff scheme worked quite well.  It gave me energies
> that were ~1% different from those of the PME calculation, which I think
> compares quite well.  The 10-ps run I attempted now takes 3 seconds, instead 
> of
> 20 minutes.
>
> Thanks to everyone for the suggestions.
>
> -Justin
>
> Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
>
>>
>> Thanks to everyone for the insights.  I'll try running things with the cutoff
>> and see how it goes.
>>
>> -Justin
>>
>> Quoting Michael Shirts <[EMAIL PROTECTED]>:
>>
>> > Hi, Justin-
>> >
>> > Have you considered -not- running PME in vacuo?  If you set your
>> > cutoffs and rlist large enough, then you can just run with simple
>> > cutoffs, and it should run -fst-.  Of course, you should compare
>> > to the energy with PME -- if they are not equivalent, then you many
>> > need to go back and check your PME parameters for accuracy.
>> >
>> > Best,
>> > Michael
>> >
>> > > I'm running some free energy calculations (in vacuo and in solution) for
>> a
>> > set
>> > > of molecules I am trying to parameterize.  All the molecules are fairly
>> > small,
>> > > about 30-35 atoms in each.  The solvated calculations go smoothly, and
>> > rather
>> > > quickly (~5 hr/ns on two nodes).  I am running into a problem when I do
>> the
>> > in
>> > > vacuo calculations.  Since I am constraining all bonds, I am running
>> things
>> > on
>> > > a local machine in the lab (single core AMD64 Opteron).  I get as far as
>> > NVT
>> > > equilibration (removing charges only) before I give up and kill it, since
>> > it
>> > > takes so long.  A 10-ps NVT run takes about 20 minutes, but that adds up
>> to
>> > > over 5 days for my 5-ns production run!  The machine is no slouch; I have
>> > used
>> > > it to run other small NVT/NPT/MD runs with good performance.  I get
>> similar
>> > > performance on another machine that is even faster (a single CPU of the
>> > 2-CPU
>> > > node on our supercomputer).  The installations of Gromacs on both are
>> fine,
>> > as
>> > > far as I can tell, and both have been used extensively.
>> > >
>> > > I am using Gromacs version 3.3.3, and I have attached my .mdp file and
>> the
>> > tail
>> > > end of my log file for reference.  If anyone notices anything obvious
>> that
>> > I'm
>> > > doing wrong, I would be grateful if you pointed it out!  I see in the log
>> > of
>> > > the slow run (in vacuo) that the 3D-FFT calculation is dominating the CPU
>> > > usage.  Is that indicative of any problem?
>> > >
>> > > Thanks for your attention.
>> > ___
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>> > Please search the archive at http://www.gromacs.org/search before posting!
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>> >
>>
>>
>>
>> 
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> [EMAIL PROTECTED] | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> 
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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>>
>
>
>
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL