date:20161121

Re: [gmx-users] FEP vs PMF

2016-11-21 Thread Alex

what I have as PMF itself has been already harvested from gmx wham.
Regards

On Mon, Nov 21, 2016 at 10:24 PM, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> You could also do WHAM analysis with gmx wham. :)
>
> On 22 November 2016 at 07:48, Alex  wrote:
>
> > Yes, indeed the thermodynamic cycle is closed.
> > If I am not wrong an integration like below should be done over PMF in
> > order to get adsorption energy which is equivalent to \Delta\Delta G in
> > FEP.
> >
> > \Delta F_{ads} = -K_{B}*T Log[ Integrate(exp(-PMF/K_{B}*T)/L)]
> >
> > in which L is the interval where PMF starts to its plateau.
> >
> > Regards,
> >
> > Alex
> >
> > On Mon, Nov 21, 2016 at 9:24 PM, Billy Williams-Noonan <
> > billy.williams-noo...@monash.edu> wrote:
> >
> > > Assuming you have closed the thermodynamic cycle correctly (which no
> > doubt
> > > you have), then I would think you have just measured the same quantity
> > with
> > > absolute FEP as you did using PMF with umbrella sampling.  You have the
> > > same dG of binding, but with different methods. :-)
> > >
> > > Cheers,
> > >
> > > Billy
> > >
> > > On 22 November 2016 at 07:19, Alex  wrote:
> > >
> > > > Hi Billy,
> > > >
> > > > Thanks for your response,  whatever you want to call it, it is the
> > > > difference between the free energies of the system in bonded(or
> > complex)
> > > > and unbounded(or ligand) states, so it is [\Delta G_{bounded} -
> \Delta
> > > > G_{unbounded}].
> > > >
> > > > Regards,
> > > > Alex
> > > >
> > > > On Mon, Nov 21, 2016 at 9:06 PM, Billy Williams-Noonan <
> > > > billy.williams-noo...@monash.edu> wrote:
> > > >
> > > > > If you're calculating an absolute free energy of dissociation, why
> > > would
> > > > it
> > > > > be a "\Delta\Delta G"?
> > > > >
> > > > > Kind Regards,
> > > > >
> > > > > Billy
> > > > >
> > > > > On 22 November 2016 at 04:12, Alex 
> > wrote:
> > > > >
> > > > > > Dear gromacs user,
> > > > > >
> > > > > > For a reaction (dissociation of a amino acid from a solid surface
> > in
> > > > > > aqueous solution), I have calculated the "\Delta\Delta G" by free
> > > > energy
> > > > > > perturbation method in alchemical analysis, and also for the same
> > > > > reaction
> > > > > > I have calculated the PMF by umbrella sampling.
> > > > > >
> > > > > > I was wondering how I can compare these two results together?
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Regards,
> > > > > > Alex
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > >
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> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
> > > > >
> > > > > *LinkedIn Profile
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> > > > >
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> > > > > Royal Parade, Parkville, 3052
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> > >
> > >
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> > >
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Re: [gmx-users] FEP vs PMF

2016-11-21 Thread Billy Williams-Noonan

You could also do WHAM analysis with gmx wham. :)

On 22 November 2016 at 07:48, Alex  wrote:

> Yes, indeed the thermodynamic cycle is closed.
> If I am not wrong an integration like below should be done over PMF in
> order to get adsorption energy which is equivalent to \Delta\Delta G in
> FEP.
>
> \Delta F_{ads} = -K_{B}*T Log[ Integrate(exp(-PMF/K_{B}*T)/L)]
>
> in which L is the interval where PMF starts to its plateau.
>
> Regards,
>
> Alex
>
> On Mon, Nov 21, 2016 at 9:24 PM, Billy Williams-Noonan <
> billy.williams-noo...@monash.edu> wrote:
>
> > Assuming you have closed the thermodynamic cycle correctly (which no
> doubt
> > you have), then I would think you have just measured the same quantity
> with
> > absolute FEP as you did using PMF with umbrella sampling.  You have the
> > same dG of binding, but with different methods. :-)
> >
> > Cheers,
> >
> > Billy
> >
> > On 22 November 2016 at 07:19, Alex  wrote:
> >
> > > Hi Billy,
> > >
> > > Thanks for your response,  whatever you want to call it, it is the
> > > difference between the free energies of the system in bonded(or
> complex)
> > > and unbounded(or ligand) states, so it is [\Delta G_{bounded} - \Delta
> > > G_{unbounded}].
> > >
> > > Regards,
> > > Alex
> > >
> > > On Mon, Nov 21, 2016 at 9:06 PM, Billy Williams-Noonan <
> > > billy.williams-noo...@monash.edu> wrote:
> > >
> > > > If you're calculating an absolute free energy of dissociation, why
> > would
> > > it
> > > > be a "\Delta\Delta G"?
> > > >
> > > > Kind Regards,
> > > >
> > > > Billy
> > > >
> > > > On 22 November 2016 at 04:12, Alex 
> wrote:
> > > >
> > > > > Dear gromacs user,
> > > > >
> > > > > For a reaction (dissociation of a amino acid from a solid surface
> in
> > > > > aqueous solution), I have calculated the "\Delta\Delta G" by free
> > > energy
> > > > > perturbation method in alchemical analysis, and also for the same
> > > > reaction
> > > > > I have calculated the PMF by umbrella sampling.
> > > > >
> > > > > I was wondering how I can compare these two results together?
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Regards,
> > > > > Alex
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
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> > > > >
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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
> > > >
> > > > *LinkedIn Profile
> > > >  > > > trk=prof-0-sb-preview-primary-button>
> > > > **|*   +61420 382 557
> > > >
> > > > Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> > > > Royal Parade, Parkville, 3052
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> >
> >
> >
> > --
> > Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
> >
> > *LinkedIn Profile
> >  > trk=prof-0-sb-preview-primary-button>
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> >
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[gmx-users] Melting temperature for the lipid bilayer

2016-11-21 Thread Mohsen Ramezanpour

Dear gromacs users,

Running simulation on a lipid bilayer made by Charmm-GUI, there is about 24
degrees difference between the reported temperature in Avanti and what I
see in my simulations for getting a liquid disordered (L_disorder) bilayer.

I am using all-atom Charmm36 FF for simulations.
I know that it is not possible to get an exact match between experimental
and simulation T values for L_alpha phase of bilayers, but I am not sure if
these gap seems reasonable or there is something wrong in my simulations. I
have checked the bonds in tails and apparently, everything looks fine with
topology.

However, based on this, doing simulation in L_alpha phase requires hight T
values (close to 85 or 90 degrees of centigrade) which makes me worry about
the water molecules in the system. It is a high temperature for water
molecules.

Its worth mentioning that bilayer structural properties like lipid order
parameters match available experimental data for these high T values.

Please let me know your opinion.

Cheers
Mohsen

-- 
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Re: [gmx-users] FEP vs PMF

2016-11-21 Thread Billy Williams-Noonan

Assuming you have closed the thermodynamic cycle correctly (which no doubt
you have), then I would think you have just measured the same quantity with
absolute FEP as you did using PMF with umbrella sampling.  You have the
same dG of binding, but with different methods. :-)

Cheers,

Billy

On 22 November 2016 at 07:19, Alex  wrote:

> Hi Billy,
>
> Thanks for your response,  whatever you want to call it, it is the
> difference between the free energies of the system in bonded(or complex)
> and unbounded(or ligand) states, so it is [\Delta G_{bounded} - \Delta
> G_{unbounded}].
>
> Regards,
> Alex
>
> On Mon, Nov 21, 2016 at 9:06 PM, Billy Williams-Noonan <
> billy.williams-noo...@monash.edu> wrote:
>
> > If you're calculating an absolute free energy of dissociation, why would
> it
> > be a "\Delta\Delta G"?
> >
> > Kind Regards,
> >
> > Billy
> >
> > On 22 November 2016 at 04:12, Alex  wrote:
> >
> > > Dear gromacs user,
> > >
> > > For a reaction (dissociation of a amino acid from a solid surface in
> > > aqueous solution), I have calculated the "\Delta\Delta G" by free
> energy
> > > perturbation method in alchemical analysis, and also for the same
> > reaction
> > > I have calculated the PMF by umbrella sampling.
> > >
> > > I was wondering how I can compare these two results together?
> > >
> > > Thanks,
> > >
> > > Regards,
> > > Alex
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
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> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
> >
> > *LinkedIn Profile
> >  > trk=prof-0-sb-preview-primary-button>
> > **|*   +61420 382 557
> >
> > Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> > Royal Parade, Parkville, 3052
> > --
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-- 
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*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] FEP vs PMF

2016-11-21 Thread Alex

Hi Billy,

Thanks for your response,  whatever you want to call it, it is the
difference between the free energies of the system in bonded(or complex)
and unbounded(or ligand) states, so it is [\Delta G_{bounded} - \Delta
G_{unbounded}].

Regards,
Alex

On Mon, Nov 21, 2016 at 9:06 PM, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> If you're calculating an absolute free energy of dissociation, why would it
> be a "\Delta\Delta G"?
>
> Kind Regards,
>
> Billy
>
> On 22 November 2016 at 04:12, Alex  wrote:
>
> > Dear gromacs user,
> >
> > For a reaction (dissociation of a amino acid from a solid surface in
> > aqueous solution), I have calculated the "\Delta\Delta G" by free energy
> > perturbation method in alchemical analysis, and also for the same
> reaction
> > I have calculated the PMF by umbrella sampling.
> >
> > I was wondering how I can compare these two results together?
> >
> > Thanks,
> >
> > Regards,
> > Alex
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
>  trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
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Re: [gmx-users] FEP vs PMF

2016-11-21 Thread Billy Williams-Noonan

If you're calculating an absolute free energy of dissociation, why would it
be a "\Delta\Delta G"?

Kind Regards,

Billy

On 22 November 2016 at 04:12, Alex  wrote:

> Dear gromacs user,
>
> For a reaction (dissociation of a amino acid from a solid surface in
> aqueous solution), I have calculated the "\Delta\Delta G" by free energy
> perturbation method in alchemical analysis, and also for the same reaction
> I have calculated the PMF by umbrella sampling.
>
> I was wondering how I can compare these two results together?
>
> Thanks,
>
> Regards,
> Alex
> --
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-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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[gmx-users] FEP vs PMF

2016-11-21 Thread Alex

Dear gromacs user,

For a reaction (dissociation of a amino acid from a solid surface in
aqueous solution), I have calculated the "\Delta\Delta G" by free energy
perturbation method in alchemical analysis, and also for the same reaction
I have calculated the PMF by umbrella sampling.

I was wondering how I can compare these two results together?

Thanks,

Regards,
Alex
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Re: [gmx-users] GTX 1070 Performance

2016-11-21 Thread Szilárd Páll

On Sat, Nov 19, 2016 at 11:39 AM, Nikhil Maroli  wrote:
> Dear all,
> We have 3x GTX 1070 and 2x 12 core Xeon processor.
>
> My simulation system consists of 540 amino acids +ligand in water.Total
> number of atoms excluding water is ~8000.Charmm36 ff and time step of 100ps.
>
> i tested small time simulation in 2 GPU card with the following command
>
> gmx mdrun -v -ntmpi 2 -ntomp 24 -deffnm md_0_1 -gpu_id 03
>
>
> I got 50ns/day ,but as per the benchmark results and few previous mails in
> mailing list with 2 x 1070 cards i must get ~100ns/day.

Must? Do you mean that with the same hardware and inputs someone else
got 100 ns/day?

Also, it looks like mdrun can't load-balance your system; you could
try a 2D decomposition with >4 ranks.

--
Szilárd

>
> Gromacs installed with GPU=on flag ,Do i need to install with MPI+GPU on
> flag to achieve better performance ? or any other advice to get better
> performance with 2 and 3 GPU Cards.
>
>
> I have attached the log file.
>
> https://drive.google.com/file/d/0BxaQk_pcR9viSE1xWUM1Z1EtZkU/view?usp=sharing
>
>
> --
> Regards,
> Nikhil Maroli
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[gmx-users] Problems with non standar residue combining Amber and GAFF

2016-11-21 Thread Rebeca García Fandiño

Dear Gromacs users,

I am trying to add a new residue into a peptide composed of standar residues. 
For that I have used Antechamber to get a starting topology for that residue, 
obtained the corresponding .itp file in GROMACS (using amb2gmx.pl) and then 
modified the corresponding files in Amber99sb.ff force field (aminoacids.rtp, 
aminoacids.arn, atomtypes.dat, etc) incorporating the information of this new 
residue.

In a first approximation I have tried to include directly the file gaff.dat 
into forcefield.itp (#include "gaff.dat"), but then I also separated the 
different sections of gaff.dat and tried to included into ffbonded.itp file 
separately. In both cases pdb2gmx works without errors. However, when I execute 
grompp, I get errors complaing about gaff parameters (for example "   Too few 
gb parameters for type br-br").


I have noticed that the type of data of gaff.dat file is not the same than the 
both files is not the same than that found in ffbonded.itp. For example, in 
ffbonded.itp from Amber:


[ bondtypes ]
; ij  func   b0  kb
  C  C  1 0.1525   259408.0 ; new99
  C  OS 1 0.1323   376560.0 ; new99
  C  H4 1 0.1080   307105.6 ; new99
(...)

whereas the analogous section in gaff.dat is:

ow-hw  553.00.9572  TIP3P water
br-br  123.22.542SOURCE1 40.0.
br-c   240.31.946SOURCE2 20.02850.0285
br-c1  352.71.787SOURCE2 40.00220.0024
(...)

So, I suppose my errors come from the  non correct definition of bondtypes, etc 
of the gaff parameters from my new residue.

How could I properly translate the information contained in gaff.dat to the 
files ffbonded.itp in Amber?

Thanks a lot for your help.

Best wishes,

Rebeca

Dr. Rebeca Garcia
Santiago de Compostela University
Spain


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[gmx-users] REMD analysis

2016-11-21 Thread Kalyanashis Jana

Dear all,

I have performed an REMD simulation for protein drug system (8350 + 32500
sol) using gromacs-4.4.5 package. But I could not understand how to do
analysis of REMD. I have used 10 set of replicas (298 K to 308.31K with
r=1.0038, the common ratio of the geometric progression)  for REMD
simulation and carried out a 5 ns simulation. I would like to compare the
thermodynamics of two drug molecules using REMD. Can you please suggest me,
how can I plot potential energy vs probability or how can I get free energy
profile? What types of analysis do I need to understand REMD?

Looking forward to hear from you.

Thanks in advance,

Kalyanashis Jana
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