Re: [gmx-users] Free energy calculation of Histone

[Justin Lemkul]

On 1/10/19 2:17 AM, Mark Abraham wrote:

Hi,

That's the wrong way around. :-) One doesn't do a lab experiment first and
then decide what you wanted to observe from it, to either :-). There are
tutorials for computing free energy of solvation, which I suggest you
follow, and I suspect your fully solvated simulation won't be useful for
that.


Note, however, that the alchemical approach that most tutorials use 
would never converge for something as large as a histone, let alone even 
a moderately sized polypeptide. MM/PBSA post-processing might be useful, 
but the values will be astronomical, as would (likely) the error bars.


-Justin


Mark

On Thu., 10 Jan. 2019, 02:45 Ayesha Kanwal, 
wrote:


Dear all users,
I am new for using GROMACS. and also read the tutorial of Methane and
water. I have already simulated data of 100 ns for four histones. I want to
know how to calculate free energy solvation from this data. which topology
file and coordinate files I will use?
I will appreciate your good suggestions.

Regards
Ayesha

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Lab: 303 Engel Hall

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Re: [gmx-users] Free energy calculation of Histone

[Mark Abraham]

Hi,

That's the wrong way around. :-) One doesn't do a lab experiment first and
then decide what you wanted to observe from it, to either :-). There are
tutorials for computing free energy of solvation, which I suggest you
follow, and I suspect your fully solvated simulation won't be useful for
that.

Mark

On Thu., 10 Jan. 2019, 02:45 Ayesha Kanwal, 
wrote:

> Dear all users,
> I am new for using GROMACS. and also read the tutorial of Methane and
> water. I have already simulated data of 100 ns for four histones. I want to
> know how to calculate free energy solvation from this data. which topology
> file and coordinate files I will use?
> I will appreciate your good suggestions.
>
> Regards
> Ayesha
>
> --
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Re: [gmx-users] Free Energy calculation

[Anjali Patel]

Hello,

Thank you for the quick reply @ Mark Abraham. I am describing in detail
what i want to do. I have taken SWCNT (12*12)and encapsulate the molecule.
Now i want to check its binding free energy. I checked reference manual to
arrange the right order but didn’t success. can anyone have any other link
or example file. I am stuck over here. please help to solve this.


With regards
Anjali Patel
Research Scholar
Department of Physics
The M S University of Baroda, Vadodara-390002
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Re: [gmx-users] Free energy calculation

[Sheikh Imamul Hossain]

Hi Michael,
Thank you for your valuable advice.
Regards
Imamul


Sincerely Your’s
*Sheikh Imamul Hossain*
PhD Research Student

Mechanical Engineering | School of Chemistry, Physics and Mechanical
Engineering | Faculty of Science and Engineering | Queensland University of
Technology| 2 George St Brisbane | GPO Box 2434 Brisbane, Queensland,
 Australia 4001
phone: +61407258933 Office Email: s2.hoss...@.qut.edu.au

Office:   P701B, P Block, Gardens Point

On Thu, Sep 21, 2017 at 8:50 AM, Michael Shirts  wrote:

> You don't have a well-posed scientific question yet.  Come back when you've
> thought about the hypotheses you want to test, and have written out what
> you are planning to do.  Try to do the calculations yourself, and come back
> if they are not working.  This is a help discussion forum for people who
> are having trouble running Gromacs.  You haven't gotten to the point you
> are running gromacs yet!
>
> On Wed, Sep 20, 2017 at 4:13 PM, Sheikh Imamul Hossain <
> s.imamul...@gmail.com> wrote:
>
> > Hi All,
> > I am interested to calculate the free energy of coarse-grained lipid
> > monolayer which contains CG lipid, cholesterol, water and nanoparticles.
> > Any suggestions regarding Metadynamics or  Umbrella sampling? Any
> tutorial
> > that will be helpful for learning? I am trying Metadynamics learning with
> > Belfast tutorial: plumed and umbrella with Bevan Lab.
> > Thanks in advanced.
> > Regards
> > Imamul
> >
> > --
> >
> > Sincerely Your’s
> > *Sheikh Imamul Hossain*
> > PhD Research Student
> >
> > Mechanical Engineering | School of Chemistry, Physics and Mechanical
> > Engineering | Faculty of Science and Engineering | Queensland University
> of
> > Technology| 2 George St Brisbane | GPO Box 2434 Brisbane, Queensland,
> >  Australia 4001
> > phone: +61407258933 Office Email: s2.hoss...@.qut.edu.au
> >
> > Office:   P701B, P Block, Gardens Point
> > --
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Re: [gmx-users] Free energy calculation

[Michael Shirts]

You don't have a well-posed scientific question yet.  Come back when you've
thought about the hypotheses you want to test, and have written out what
you are planning to do.  Try to do the calculations yourself, and come back
if they are not working.  This is a help discussion forum for people who
are having trouble running Gromacs.  You haven't gotten to the point you
are running gromacs yet!

On Wed, Sep 20, 2017 at 4:13 PM, Sheikh Imamul Hossain <
s.imamul...@gmail.com> wrote:

> Hi All,
> I am interested to calculate the free energy of coarse-grained lipid
> monolayer which contains CG lipid, cholesterol, water and nanoparticles.
> Any suggestions regarding Metadynamics or  Umbrella sampling? Any tutorial
> that will be helpful for learning? I am trying Metadynamics learning with
> Belfast tutorial: plumed and umbrella with Bevan Lab.
> Thanks in advanced.
> Regards
> Imamul
>
> --
>
> Sincerely Your’s
> *Sheikh Imamul Hossain*
> PhD Research Student
>
> Mechanical Engineering | School of Chemistry, Physics and Mechanical
> Engineering | Faculty of Science and Engineering | Queensland University of
> Technology| 2 George St Brisbane | GPO Box 2434 Brisbane, Queensland,
>  Australia 4001
> phone: +61407258933 Office Email: s2.hoss...@.qut.edu.au
>
> Office:   P701B, P Block, Gardens Point
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

Hello Tasneem,

Same like you, I'm pretty new to this field too. I don't know enough how to
calculate free energy in gromacs. I did only MM/PBSA for binding energy
calculations.
I'll let you know if i get some thing relevant to your question.

All the best.

Thanks

On Thu, Jan 5, 2017 at 10:28 PM, tasneem kausar 
wrote:

> Dear all
>
> It is first time I am calculating free energy of protein and ligand. I am
> following the Justin's tutorial of methane in water free energy
> calculations. Though only van der waal lambda are defined so I have taken
> the mdp files from the alchemistry.org web page. Since the ligand and
> protein under my study have positive charges (one positive charge on ligand
> and tree positive charges on protein). So I have to add a CL ions in
> topology file to make a neutral sytem.
> Is it okay to use the system with ion for free energy calculation?
> If yes, What are change that can be made in mdp entry.
>
> Waiting for suggestions
> Thanks in Advance
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks again

That is it what I was asking. I have seen the topology files of t4-lysozyme
with its ligand. It was provided by alchemistry.org tutorial. Can I change
the topology accordingly.
Another thing is the charge on the ligand molecule. How this will be
handled in free energy calculations.

Waiting for your suggestion

On Sat, Jan 7, 2017 at 10:35 AM, Amir Zeb  wrote:

> well
> if you are confident of your simulation you may definitly go ahead with
> this ff
> otherwise you will have to change the ff for simulation too
> i think this is not rational to simulate the system with one ff and then
> change the ff for free energy calculations
>
> good luck
>
> On Jan 7, 2017 2:01 PM, "tasneem kausar" 
> wrote:
>
> > Thanks Amir Zeb for your reply
> > I have read in literature about the FEPsetup to parametrize the complex
> > file (protein+drug) for simulation. This setup builds files based on
> amber.
> > Since I have previously used 54a7ff to simulate the protein and drug and
> > topology files were generated from ATB in gromos54a7 format. Since I
> didn't
> > find free energy calculation of protein and ligand with this force field.
> > Thats why I was confused to proceed further using the same.
> >
> > On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <
> tasneemkausa...@gmail.com
> > >
> > wrote:
> >
> > > mm/pbsa calculates binding energy. I have used that.
> > >
> > > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
> > >
> > >> hello
> > >> you may use mm/pbsa compiled with gromacs to calculate free energy
> > >> all the best
> > >>
> > >> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> > >> wrote:
> > >>
> > >> > Dear gromacs users
> > >> >
> > >> > It is first time I am trying to perform free energy calculation of
> > >> protein
> > >> > and drug complex. I am following Justin' s tutorial of mehtane in
> > water.
> > >> > That calculation are performed on a neutral system. If the ligand
> > >> molecule
> > >> > has charge what are the provisions that could be taken into account.
> > >> > I have performed my MD simulation using force field gromos54a7. And
> > Now
> > >> I
> > >> > am trying to go onward using free energy calculations. Since the
> free
> > >> > energy calculations are performed on ambed99ldn, opls and charmm
> force
> > >> > fields (as I know from the articles). Is it okay to use gromos54a7
> ff
> > >> for
> > >> > free energy calculations.
> > >> >
> > >> > Kindly tell me
> > >> >
> > >> > Thanks in Advance
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
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> > >> > Support/Mailing_Lists/GMX-Users_List before posting!
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> > >> >
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

well
if you are confident of your simulation you may definitly go ahead with
this ff
otherwise you will have to change the ff for simulation too
i think this is not rational to simulate the system with one ff and then
change the ff for free energy calculations

good luck

On Jan 7, 2017 2:01 PM, "tasneem kausar"  wrote:

> Thanks Amir Zeb for your reply
> I have read in literature about the FEPsetup to parametrize the complex
> file (protein+drug) for simulation. This setup builds files based on amber.
> Since I have previously used 54a7ff to simulate the protein and drug and
> topology files were generated from ATB in gromos54a7 format. Since I didn't
> find free energy calculation of protein and ligand with this force field.
> Thats why I was confused to proceed further using the same.
>
> On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar  >
> wrote:
>
> > mm/pbsa calculates binding energy. I have used that.
> >
> > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
> >
> >> hello
> >> you may use mm/pbsa compiled with gromacs to calculate free energy
> >> all the best
> >>
> >> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> >> wrote:
> >>
> >> > Dear gromacs users
> >> >
> >> > It is first time I am trying to perform free energy calculation of
> >> protein
> >> > and drug complex. I am following Justin' s tutorial of mehtane in
> water.
> >> > That calculation are performed on a neutral system. If the ligand
> >> molecule
> >> > has charge what are the provisions that could be taken into account.
> >> > I have performed my MD simulation using force field gromos54a7. And
> Now
> >> I
> >> > am trying to go onward using free energy calculations. Since the free
> >> > energy calculations are performed on ambed99ldn, opls and charmm force
> >> > fields (as I know from the articles). Is it okay to use gromos54a7 ff
> >> for
> >> > free energy calculations.
> >> >
> >> > Kindly tell me
> >> >
> >> > Thanks in Advance
> >> > --
> >> > 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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> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
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> >
> >
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks Amir Zeb for your reply
I have read in literature about the FEPsetup to parametrize the complex
file (protein+drug) for simulation. This setup builds files based on amber.
Since I have previously used 54a7ff to simulate the protein and drug and
topology files were generated from ATB in gromos54a7 format. Since I didn't
find free energy calculation of protein and ligand with this force field.
Thats why I was confused to proceed further using the same.

On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar 
wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
>
>> hello
>> you may use mm/pbsa compiled with gromacs to calculate free energy
>> all the best
>>
>> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
>> wrote:
>>
>> > Dear gromacs users
>> >
>> > It is first time I am trying to perform free energy calculation of
>> protein
>> > and drug complex. I am following Justin' s tutorial of mehtane in water.
>> > That calculation are performed on a neutral system. If the ligand
>> molecule
>> > has charge what are the provisions that could be taken into account.
>> > I have performed my MD simulation using force field gromos54a7. And Now
>> I
>> > am trying to go onward using free energy calculations. Since the free
>> > energy calculations are performed on ambed99ldn, opls and charmm force
>> > fields (as I know from the articles). Is it okay to use gromos54a7 ff
>> for
>> > free energy calculations.
>> >
>> > Kindly tell me
>> >
>> > Thanks in Advance
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
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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.
>> >
>> --
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>>
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>>
>
>
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

alright
why do you care of forcefield in terms of free energy calculations?
do you have literature in reference for your protein simulated with a
specific ff?

On Jan 7, 2017 1:38 PM, "tasneem kausar"  wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
>
> > hello
> > you may use mm/pbsa compiled with gromacs to calculate free energy
> > all the best
> >
> > On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> > wrote:
> >
> > > Dear gromacs users
> > >
> > > It is first time I am trying to perform free energy calculation of
> > protein
> > > and drug complex. I am following Justin' s tutorial of mehtane in
> water.
> > > That calculation are performed on a neutral system. If the ligand
> > molecule
> > > has charge what are the provisions that could be taken into account.
> > > I have performed my MD simulation using force field gromos54a7. And
> Now I
> > > am trying to go onward using free energy calculations. Since the free
> > > energy calculations are performed on ambed99ldn, opls and charmm force
> > > fields (as I know from the articles). Is it okay to use gromos54a7 ff
> for
> > > free energy calculations.
> > >
> > > Kindly tell me
> > >
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

mm/pbsa calculates binding energy. I have used that.

On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:

> hello
> you may use mm/pbsa compiled with gromacs to calculate free energy
> all the best
>
> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> wrote:
>
> > Dear gromacs users
> >
> > It is first time I am trying to perform free energy calculation of
> protein
> > and drug complex. I am following Justin' s tutorial of mehtane in water.
> > That calculation are performed on a neutral system. If the ligand
> molecule
> > has charge what are the provisions that could be taken into account.
> > I have performed my MD simulation using force field gromos54a7. And Now I
> > am trying to go onward using free energy calculations. Since the free
> > energy calculations are performed on ambed99ldn, opls and charmm force
> > fields (as I know from the articles). Is it okay to use gromos54a7 ff for
> > free energy calculations.
> >
> > Kindly tell me
> >
> > Thanks in Advance
> > --
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

hello
you may use mm/pbsa compiled with gromacs to calculate free energy
all the best

On Jan 7, 2017 1:27 PM, "tasneem kausar"  wrote:

> Dear gromacs users
>
> It is first time I am trying to perform free energy calculation of protein
> and drug complex. I am following Justin' s tutorial of mehtane in water.
> That calculation are performed on a neutral system. If the ligand molecule
> has charge what are the provisions that could be taken into account.
> I have performed my MD simulation using force field gromos54a7. And Now I
> am trying to go onward using free energy calculations. Since the free
> energy calculations are performed on ambed99ldn, opls and charmm force
> fields (as I know from the articles). Is it okay to use gromos54a7 ff for
> free energy calculations.
>
> Kindly tell me
>
> Thanks in Advance
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Free energy calculation

[Justin Lemkul]

On 11/28/16 9:22 AM, Khadija Amine wrote:

Could you please propound a suggestion more helpful for doing it?



MM/PBSA calculations use the MM energy and solvation free energy estimates from 
PB to give the free energy of a given conformation.  Combined with entropy 
calculations (Schlitter or quasi-harmonic approximation), you can get a decent 
estimate of the actual free energy.  The calculations neglect solvent, so if 
e.g. the solvent entropy is a significant contribution in a given system, the 
results may not be correct in an absolute sense, but for comparing point 
mutations, it's probably accurate enough.



Should I perform more MD simulation for my complexes?



As with any MD result, you need good sampling and a converged ensemble.  A 
single simulation of 20 ns is neither.


-Justin


*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 4:56 PM, Khadija Amine  wrote:


As I have mentioned in my first email, I want to calculate the free energy
of my protein-protein complex.

I want to compute free energies for wild type and mutant complex and
compare them.

*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 4:02 PM, Khadija Amine 
wrote:


Thank you Williams.

I should try the umbrella sampling tutorial?

My complex is simulated during 20ns. The starting files for free energy
computing should be the MD production files?



*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine 
wrote:


Dear Gromacs users,

I have a system of protein-protein interaction.

Is it possible to calculate the free energy of the complex?

If it so, could you please give me an efficient tool to compute the free
energy calculation.

Any suggestion. Thank you


*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University​*








--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation

[Khadija Amine]

Could you please propound a suggestion more helpful for doing it?

Should I perform more MD simulation for my complexes?

*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 4:56 PM, Khadija Amine  wrote:

> As I have mentioned in my first email, I want to calculate the free energy
> of my protein-protein complex.
>
> I want to compute free energies for wild type and mutant complex and
> compare them.
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Mon, Nov 28, 2016 at 4:02 PM, Khadija Amine 
> wrote:
>
>> Thank you Williams.
>>
>> I should try the umbrella sampling tutorial?
>>
>> My complex is simulated during 20ns. The starting files for free energy
>> computing should be the MD production files?
>>
>>
>>
>> *Khadija AMINE*
>>
>>
>> *Computational Biology*
>> *Postdoctoral Research Associate*
>> *Carnegie Mellon University*
>>
>> On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine 
>> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I have a system of protein-protein interaction.
>>>
>>> Is it possible to calculate the free energy of the complex?
>>>
>>> If it so, could you please give me an efficient tool to compute the free
>>> energy calculation.
>>>
>>> Any suggestion. Thank you
>>>
>>>
>>> *Khadija AMINE*
>>>
>>>
>>> *Computational Biology*
>>> *Postdoctoral Research Associate*
>>> *Carnegie Mellon University​*
>>>
>>
>>
>
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Re: [gmx-users] Free energy calculation

[Justin Lemkul]

On 11/28/16 8:56 AM, Khadija Amine wrote:

As I have mentioned in my first email, I want to calculate the free energy
of my protein-protein complex.



That can be a bit ambiguous.


I want to compute free energies for wild type and mutant complex and
compare them.


This is a more clearly defined objective; presumably you want to do an MM/PBSA 
analysis.  I would not expect 20 ns to be nearly enough sampling, though.


-Justin



*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 4:02 PM, Khadija Amine  wrote:


Thank you Williams.

I should try the umbrella sampling tutorial?

My complex is simulated during 20ns. The starting files for free energy
computing should be the MD production files?



*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine 
wrote:


Dear Gromacs users,

I have a system of protein-protein interaction.

Is it possible to calculate the free energy of the complex?

If it so, could you please give me an efficient tool to compute the free
energy calculation.

Any suggestion. Thank you


*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University​*






--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation

[Khadija Amine]

As I have mentioned in my first email, I want to calculate the free energy
of my protein-protein complex.

I want to compute free energies for wild type and mutant complex and
compare them.

*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 4:02 PM, Khadija Amine  wrote:

> Thank you Williams.
>
> I should try the umbrella sampling tutorial?
>
> My complex is simulated during 20ns. The starting files for free energy
> computing should be the MD production files?
>
>
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine 
> wrote:
>
>> Dear Gromacs users,
>>
>> I have a system of protein-protein interaction.
>>
>> Is it possible to calculate the free energy of the complex?
>>
>> If it so, could you please give me an efficient tool to compute the free
>> energy calculation.
>>
>> Any suggestion. Thank you
>>
>>
>> *Khadija AMINE*
>>
>>
>> *Computational Biology*
>> *Postdoctoral Research Associate*
>> *Carnegie Mellon University​*
>>
>
>
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Re: [gmx-users] Free energy calculation

[Justin Lemkul]

On 11/28/16 8:02 AM, Khadija Amine wrote:

Thank you Williams.

I should try the umbrella sampling tutorial?

My complex is simulated during 20ns. The starting files for free energy
computing should be the MD production files?




Free energy of what?  The tutorial suggested before is useful for computing a 
free energy of binding between proteins.


-Justin



*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine  wrote:


Dear Gromacs users,

I have a system of protein-protein interaction.

Is it possible to calculate the free energy of the complex?

If it so, could you please give me an efficient tool to compute the free
energy calculation.

Any suggestion. Thank you


*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University​*



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation

[Khadija Amine]

Thank you Williams.

I should try the umbrella sampling tutorial?

My complex is simulated during 20ns. The starting files for free energy
computing should be the MD production files?



*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine  wrote:

> Dear Gromacs users,
>
> I have a system of protein-protein interaction.
>
> Is it possible to calculate the free energy of the complex?
>
> If it so, could you please give me an efficient tool to compute the free
> energy calculation.
>
> Any suggestion. Thank you
>
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University​*
>
-- 
Gromacs Users mailing list

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Re: [gmx-users] Free energy calculation

[Billy Williams-Noonan]

It would probably be easiest to generate a PMF curve.  Try Justin Lemkul's
PMF tutorial and alter the box geometry as needed... :)

On 28 November 2016 at 20:56, Khadija Amine  wrote:

> Dear Gromacs users,
>
> I have a system of protein-protein interaction.
>
> Is it possible to calculate the free energy of the complex?
>
> If it so, could you please give me an efficient tool to compute the free
> energy calculation.
>
> Any suggestion. Thank you
>
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University​*
> --
> 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

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] Free energy calculation problem with too high dG

[Hannes Loeffler]

On Tue, 4 Oct 2016 15:27:25 +0300
Vlad  wrote:

> I tried to do the decoupling and strangely the result is not the same
> Below is the end of the log
> The total dG is significantly less then previous and the last dG
> value is particularly small I think total dG will get less with more
> precise lambda sampling (by 0.05 instead of 0.1) The thing which
> still is strange is the value of entropy for the last lambda (in the
> previous case it was so high as well for the first lambda)
> 
> So you suggest to use restraints
> Througout the simulation or also gradually switched off?

I suggest that you have a careful look at that web page and related
literature to understand how this type of simulation is supposed to
work. As per my previous explanation I do not see anything particularly
strange at this point.  Making a molecule disappear is just so much
simpler than making it appear.  In the latter case you may get away
with (much) longer equilibration (did you actually do prior
minimisation?).  You may also disrupt your system quite severely esp. in
the case of a protein environment.  Maybe a proper choice of positional
restraints may help.  But I am nor sure if going this route is really
worthwhile except for better understanding the method.  You will
however not get around a careful analysis of your simulations.


Cheers,
Hannes.
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Re: [gmx-users] Free energy calculation problem with too high dG

[Vlad]

I tried to do the decoupling and strangely the result is not the same
Below is the end of the log
The total dG is significantly less then previous and the last dG value is 
particularly small
I think total dG will get less with more precise lambda sampling (by 0.05 
instead of 0.1)
The thing which still is strange is the value of entropy for the last lambda 
(in the previous case it was so high as well for the first lambda)

So you suggest to use restraints
Througout the simulation or also gradually switched off?

Thank you for help

Sincerely yours,
Vlad

Temperature: 300 K
Detailed results in kT (see help for explanation):
lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 
0 1 0.66 0.02 0.03 0.00 0.03 0.00 0.21 0.00
1 2 0.62 0.01 0.01 0.01 0.01 0.01 0.21 0.00
2 3 2.15 0.04 0.29 0.04 0.29 0.04 0.79 0.01
3 4 0.82 0.01 0.11 0.02 0.11 0.02 0.38 0.00
4 5 0.69 0.01 0.02 0.01 0.02 0.01 0.35 0.01
5 6 0.58 0.01 0.09 0.01 0.09 0.01 0.35 0.01
6 7 0.42 0.01 0.08 0.01 0.08 0.01 0.34 0.01
7 8 0.28 0.01 0.06 0.01 0.06 0.01 0.33 0.01
8 9 0.20 0.01 0.02 0.02 0.02 0.01 0.31 0.00
9 10 0.13 0.03 0.05 0.02 0.05 0.02 0.32 0.01
10 11 4.19 0.02 0.06 0.02 0.06 0.02 0.22 0.01
11 12 4.13 0.04 0.00 0.01 0.00 0.01 0.21 0.01
12 13 8.13 0.05 0.14 0.05 0.14 0.05 0.46 0.01
13 14 7.87 0.02 0.11 0.03 0.12 0.03 0.49 0.02
14 15 7.67 0.03 0.09 0.03 0.10 0.03 0.51 0.02
15 16 7.38 0.04 0.19 0.05 0.20 0.05 0.57 0.03
16 17 7.09 0.09 0.08 0.06 0.10 0.06 0.62 0.01
17 18 6.67 0.08 0.33 0.06 0.36 0.06 0.75 0.03
18 19 5.95 0.04 0.36 0.04 0.46 0.05 0.90 0.03
19 20 4.62 0.05 0.87 0.11 1.39 0.16 1.51 0.06
20 21 0.49 0.07 1.12 0.07 1.73 0.12 1.68 0.05
21 22 -12.20 0.38 10.97 0.34 530033806446307904.00 343034015797650752.00 49.55 
3.92

Final results in kJ/mol:
point 0 - 1, DG 1.63 +/- 0.06
point 1 - 2, DG 1.54 +/- 0.04
point 2 - 3, DG 5.37 +/- 0.10
point 3 - 4, DG 2.04 +/- 0.03
point 4 - 5, DG 1.71 +/- 0.03
point 5 - 6, DG 1.45 +/- 0.03
point 6 - 7, DG 1.04 +/- 0.03
point 7 - 8, DG 0.69 +/- 0.02
point 8 - 9, DG 0.50 +/- 0.03
point 9 - 10, DG 0.33 +/- 0.07
point 10 - 11, DG 10.44 +/- 0.04
point 11 - 12, DG 10.30 +/- 0.09
point 12 - 13, DG 20.27 +/- 0.12
point 13 - 14, DG 19.64 +/- 0.04
point 14 - 15, DG 19.13 +/- 0.07
point 15 - 16, DG 18.40 +/- 0.10
point 16 - 17, DG 17.70 +/- 0.22
point 17 - 18, DG 16.64 +/- 0.20
point 18 - 19, DG 14.85 +/- 0.10
point 19 - 20, DG 11.53 +/- 0.12
point 20 - 21, DG 1.23 +/- 0.19
point 21 - 22, DG -30.43 +/- 0.94
total 0 - 22, DG 146.01 +/- 0.95
 


>Вторник,  4 октября 2016, 15:15 +03:00 от Hannes Loeffler 
>:
>
>On Tue, 4 Oct 2016 14:01:52 +0300
>Vlad < vlad_bal...@mail.ru > wrote:
>> No reason. I just thought it would give the same result. 
>
>In theory both directions should be symmetrical and give the same
>result.
>
>
>> In the trajectory the ligand diffuse to the end of the cell like a
>> ghost through the water molecules. And could the reason lie in the
>> fact that in the initial structure during all preparations the ligand
>> is "fully existing" and in the first step of simulation suddenly is
>> turned off? 
>
>
>I would suggest to have a look through
>http://www.alchemistry.org/wiki/Example:_Absolute_Binding_Affinity and
>other material on that web page.  In particular reference 1 on that
>page should be of interest to you in how to use restraints within a
>general scheme.
>
>In a homogeneous environment like water it doesn't matter that your
>"ghost" molecule drifts because on average the interactions with its
>environment will be the same regardless of location.  In an
>inhomogeneous environment, however, the nearly non-interacting ligand
>will have different probabilities of where it is located.  In
>principle, you would have to sample _all_ possible locations which in
>practice is hard or impossible.  Hence the restraint scheme as
>suggested above.
>
>Your ligand should exists as a bonded network throughout the
>simulation.  What you are doing however is "decoupling" which means
>that the non-bonded interactions between the ligand and its environment
>and vice versa a gradually switched off.
>
>
>Cheers,
>Hannes.
>-- 
>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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Re: [gmx-users] Free energy calculation problem with too high dG

[Hannes Loeffler]

On Tue, 4 Oct 2016 14:01:52 +0300
Vlad  wrote:
> No reason. I just thought it would give the same result.  

In theory both directions should be symmetrical and give the same
result.


> In the trajectory the ligand diffuse to the end of the cell like a
> ghost through the water molecules. And could the reason lie in the
> fact that in the initial structure during all preparations the ligand
> is "fully existing" and in the first step of simulation suddenly is
> turned off?  


I would suggest to have a look through
http://www.alchemistry.org/wiki/Example:_Absolute_Binding_Affinity and
other material on that web page.  In particular reference 1 on that
page should be of interest to you in how to use restraints within a
general scheme.

In a homogeneous environment like water it doesn't matter that your
"ghost" molecule drifts because on average the interactions with its
environment will be the same regardless of location.  In an
inhomogeneous environment, however, the nearly non-interacting ligand
will have different probabilities of where it is located.  In
principle, you would have to sample _all_ possible locations which in
practice is hard or impossible.  Hence the restraint scheme as
suggested above.

Your ligand should exists as a bonded network throughout the
simulation.  What you are doing however is "decoupling" which means
that the non-bonded interactions between the ligand and its environment
and vice versa a gradually switched off.


Cheers,
Hannes.
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Re: [gmx-users] Free energy calculation problem with too high dG

[Vlad]

No reason. I just thought it would give the same result. Now I launched a 
simulation with decoupling (without md and with few number of lambda values - 
only for testing). Hope it will end in an hour

In the trajectory the ligand diffuse to the end of the cell like a ghost 
through the water molecules.
And could the reason lie in the fact that in the initial structure during all 
preparations the ligand is "fully existing" and in the first step of simulation 
suddenly is turned off?

Sincerely yours,
Vlad

>Вторник,  4 октября 2016, 13:50 +03:00 от Hannes Loeffler 
>:
>
>On Tue, 4 Oct 2016 13:08:51 +0300
>Vlad < vlad_bal...@mail.ru > wrote:
>
>> It appears in the step where ligand starts to recouple (I start
>> from the decoupled ligand and consequently turn on vdw and then
>> charges). And the dG between the zero and the first init_lambda
>> appears about 1800 kJ/mol
>
>Is there any particular reason why you cannot run a decoupling
>simulation?  Creating a molecule out of "nothing" will need to push
>existing atoms aside and I can see why that could be a problem. 
>Have you checked the trajectory to see what is happening?
>
>
>Cheers,
>Hannes.


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Re: [gmx-users] Free energy calculation problem with too high dG

[Hannes Loeffler]

On Tue, 4 Oct 2016 13:08:51 +0300
Vlad  wrote:

> It appears in the step where ligand starts to recouple (I start
> from the decoupled ligand and consequently turn on vdw and then
> charges). And the dG between the zero and the first init_lambda
> appears about 1800 kJ/mol

Is there any particular reason why you cannot run a decoupling
simulation?  Creating a molecule out of "nothing" will need to push
existing atoms aside and I can see why that could be a problem.  
Have you checked the trajectory to see what is happening?


Cheers,
Hannes.
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[Sun Iba]

The single code from script reproduced the same error:

C































*ommand line:  gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp
-c /home/Documents/tutorial/Methane/methane_water.gro -p
/home/Documents/tutorial/Methane/topol.top -o
min.tpr---Program gmx,
VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/futil.cpp, line:
540File input/output error:/home/Documents/tutorial/MDP/EM/em_steep.mdpFor
more information and tips for troubleshooting, please check the
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>---
GROMACS:  gmx mdrun, VERSION 5.0Executable:
/usr/local/gromacs/bin/gmxLibrary dir:
/usr/local/gromacs/share/gromacs/topCommand line:  mdrun -nt 2 -deffnm
min0Back Off! I just backed up min0.log to
./#min0.log.5#---Program
mdrun, VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line:
513Can not open file:min0.tprFor more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentati <http://www.gromacs.org/Documentati>*
on/Errors
---


However, I tried using normal command i.e. gmx grompp and dint use the
script and the command worked smoothly. The first minimization step is
complete. I dont know why there is "File input/output" error with script. I
have placed the .mdp files in /home/Docuemnts/tutorial/MDP/EM, as I
mentioned in .sh file:


#!/bin/bash

# Set some environment variables
FREE_ENERGY=/home/Documents/tutorial
echo "Free energy home directory set to $FREE_ENERGY"

MDP=$FREE_ENERGY/MDP/EM
echo ".mdp files are stored in $MDP"

LAMBDA=0

# A new directory will be created for each value of lambda and
# at each step in the workflow for maximum organization.

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

#
# ENERGY MINIMIZATION 1: STEEP  #
#
echo "Starting minimization for lambda = $LAMBDA..."

mkdir EM_1
cd EM_1

# Iterative calls to grompp and mdrun to run the simulations

gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c
$FREE_ENERGY/Methane/methane_water.gro
-p $FREE_ENERGY/Methane/topol.top -o min$LAMBDA.tpr

mdrun -nt 2 -deffnm min$LAMBDA

sleep 10


*Have I messed up with the job.sh?*

On Sat, Sep 3, 2016 at 10:00 AM, sun.iba2  wrote:

> Yes. Doing that. Thank you very much.
>
>
> Sent from Samsung Mobile
>
>
>  Original message 
> From: Nikhil Maroli 
> Date:02/09/2016 7:28 PM (GMT+05:30)
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Cc:
> Subject: Re: [gmx-users] Free energy calculation, Methane in water
> tutorial
>
> run the single code from script and see what prints on the screen,that's
> what Justin suggested
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[Sun Iba]

The single code from script reproduced the same error:

C





















































*ommand line:  gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp
-c /home/Documents/tutorial/Methane/methane_water.gro -p
/home/Documents/tutorial/Methane/topol.top -o
min.tpr---Program gmx,
VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/futil.cpp, line:
540File input/output error:/home/Documents/tutorial/MDP/EM/em_steep.mdpFor
more information and tips for troubleshooting, please check the
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
---GROMACS:
gmx mdrun, VERSION 5.0GROMACS is written by:Emile Apol Rossen
Apostolov   Herman J.C. Berendsen Par Bjelkmar   Aldert van Buuren
Rudi van DrunenAnton Feenstra Sebastian Fritsch  Gerrit Groenhof
Christoph Junghans Peter Kasson   Carsten KutznerPer Larsson
Justin A. Lemkul   Magnus LundborgPieter Meulenhoff  Erik Marklund
Teemu Murtola  Szilard Pall   Sander Pronk   Roland Schulz
Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman
Christian Wennberg Maarten Wolf   and the project leaders:Mark Abraham,
Berk Hess, Erik Lindahl, and David van der SpoelCopyright (c) 1991-2000,
University of Groningen, The Netherlands.Copyright (c) 2001-2014, The
GROMACS development team atUppsala University, Stockholm University andthe
Royal Institute of Technology, Sweden.check out http://www.gromacs.org
 for more information.GROMACS is free software; you
can redistribute it and/or modify itunder the terms of the GNU Lesser
General Public Licenseas published by the Free Software Foundation; either
version 2.1of the License, or (at your option) any later
version.GROMACS:  gmx mdrun, VERSION 5.0Executable:
/usr/local/gromacs/bin/gmxLibrary dir:
/usr/local/gromacs/share/gromacs/topCommand line:  mdrun -nt 2 -deffnm
min0Back Off! I just backed up min0.log to
./#min0.log.5#---Program
mdrun, VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line:
513Can not open file:min0.tprFor more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentati *
on/Errors
---


However, I tried using normal command i.e. I dint use the script and the
command worked smoothly. The minimization step is complete. I dont know why
there is "File input/output" error. I have placed the .mdp files in
/home/Docuemnts/tutorial/MDP/EM, as I mentioned in .sh file:


#!/bin/bash

# Set some environment variables
FREE_ENERGY=/home/Documents/tutorial
echo "Free energy home directory set to $FREE_ENERGY"

MDP=$FREE_ENERGY/MDP/EM
echo ".mdp files are stored in $MDP"

LAMBDA=0

# A new directory will be created for each value of lambda and
# at each step in the workflow for maximum organization.

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

#
# ENERGY MINIMIZATION 1: STEEP  #
#
echo "Starting minimization for lambda = $LAMBDA..."

mkdir EM_1
cd EM_1

# Iterative calls to grompp and mdrun to run the simulations

gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c
$FREE_ENERGY/Methane/methane_water.gro -p $FREE_ENERGY/Methane/topol.top -o
min$LAMBDA.tpr

mdrun -nt 2 -deffnm min$LAMBDA

sleep 10


Have I messed up the job.sh?

On Fri, Sep 2, 2016 at 7:28 PM, Nikhil Maroli  wrote:

> run the single code from script and see what prints on the screen,that's
> what Justin suggested
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[sun.iba2]

Yes. I am doing that now. Thank you  ery much.


Sent from Samsung Mobile

 Original message From: Justin Lemkul 
 Date:02/09/2016  8:01 PM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Free energy calculation, Methane in water tutorial 


On 9/2/16 9:53 AM, sun.iba2 wrote:
> Yes. But nothing else is printed on screen. Log files are creared but 
> incomplete. When I used perl script to generate respective .mdp files for 
> mininization and equilibrium, i found all of the generated files for 21 
> lambda values were empty. However when I tried with my molecule, the 21 .mdp 
> files are created properly but still encountered same error with my file i.e. 
> .tpr file is missing.
>

This suggests something at the very top level is not set up correctly (paths, 
environment variables, etc).  Run the commands in the job script interactively 
to figure out which step is failing.

-Justin

>
>
>
>
>  Original message From: Justin Lemkul 
>  Date:02/09/2016  4:57 PM  (GMT+05:30) 
> To: gmx-us...@gromacs.org Cc:  Subject: Re: 
> [gmx-users] Free energy calculation, Methane in water tutorial 
> 
>
> On 9/2/16 7:09 AM, Sun Iba wrote:
>> Hello dear users
>>
>> I am following Justin's tutorial for free energy calculation of Methane in
>> water. I have downloaded the job.sh file and trying to run it in terminal
>> using: sh job.sh but it is giving following error:
>>
>> Program mdrun, VERSION 5.0
>> Source code file:
>> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
>>
>> Can not open file:
>> min0.tpr
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> Please help me with error.
>>
>
> grompp failed to produce the .tpr file.  Use the screen output to figure out 
> why.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[sun.iba2]

Yes. Doing that. Thank you very much.


Sent from Samsung Mobile

 Original message From: Nikhil Maroli 
 Date:02/09/2016  7:28 PM  (GMT+05:30) 
To: gromacs.org_gmx-users@maillist.sys.kth.se Cc:  
Subject: Re: [gmx-users] Free energy calculation, Methane in water 
tutorial 
run the single code from script and see what prints on the screen,that's
what Justin suggested
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[Justin Lemkul]

On 9/2/16 9:53 AM, sun.iba2 wrote:

Yes. But nothing else is printed on screen. Log files are creared but 
incomplete. When I used perl script to generate respective .mdp files for 
mininization and equilibrium, i found all of the generated files for 21 lambda 
values were empty. However when I tried with my molecule, the 21 .mdp files are 
created properly but still encountered same error with my file i.e. .tpr file 
is missing.



This suggests something at the very top level is not set up correctly (paths, 
environment variables, etc).  Run the commands in the job script interactively 
to figure out which step is failing.


-Justin






 Original message From: Justin Lemkul  Date:02/09/2016  4:57 PM  
(GMT+05:30) To: gmx-us...@gromacs.org Cc:  Subject: Re: [gmx-users] Free energy calculation, 
Methane in water tutorial 


On 9/2/16 7:09 AM, Sun Iba wrote:

Hello dear users

I am following Justin's tutorial for free energy calculation of Methane in
water. I have downloaded the job.sh file and trying to run it in terminal
using: sh job.sh but it is giving following error:

Program mdrun, VERSION 5.0
Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513

Can not open file:
min0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Please help me with error.



grompp failed to produce the .tpr file.  Use the screen output to figure out 
why.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[Nikhil Maroli]

run the single code from script and see what prints on the screen,that's
what Justin suggested
-- 
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[sun.iba2]

@Gozde..yes the.tpr file is not produced. I am looking at it. Will try again.
Thank you


Sent from Samsung Mobile

 Original message From: gozde ergin 
 Date:02/09/2016  4:56 PM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Free energy calculation, Methane in water tutorial 
The error is pretty clear. Do you produce the min0.tpr file?
Where do you put this file? Is it in the same directory of job.sh file?

> On 02 Sep 2016, at 13:09, Sun Iba  wrote:
> 
> Hello dear users
> 
> I am following Justin's tutorial for free energy calculation of Methane in
> water. I have downloaded the job.sh file and trying to run it in terminal
> using: sh job.sh but it is giving following error:
> 
> Program mdrun, VERSION 5.0
> Source code file:
> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
> 
> Can not open file:
> min0.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Please help me with error.
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[sun.iba2]

Yes. But nothing else is printed on screen. Log files are creared but 
incomplete. When I used perl script to generate respective .mdp files for 
mininization and equilibrium, i found all of the generated files for 21 lambda 
values were empty. However when I tried with my molecule, the 21 .mdp files are 
created properly but still encountered same error with my file i.e. .tpr file 
is missing. 





 Original message From: Justin Lemkul 
 Date:02/09/2016  4:57 PM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Free energy calculation, Methane in water tutorial 


On 9/2/16 7:09 AM, Sun Iba wrote:
> Hello dear users
>
> I am following Justin's tutorial for free energy calculation of Methane in
> water. I have downloaded the job.sh file and trying to run it in terminal
> using: sh job.sh but it is giving following error:
>
> Program mdrun, VERSION 5.0
> Source code file:
> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
>
> Can not open file:
> min0.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Please help me with error.
>

grompp failed to produce the .tpr file.  Use the screen output to figure out 
why.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[Justin Lemkul]

On 9/2/16 7:09 AM, Sun Iba wrote:

Hello dear users

I am following Justin's tutorial for free energy calculation of Methane in
water. I have downloaded the job.sh file and trying to run it in terminal
using: sh job.sh but it is giving following error:

Program mdrun, VERSION 5.0
Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513

Can not open file:
min0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Please help me with error.



grompp failed to produce the .tpr file.  Use the screen output to figure out 
why.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation, Methane in water tutorial

[gozde ergin]

The error is pretty clear. Do you produce the min0.tpr file?
Where do you put this file? Is it in the same directory of job.sh file?

> On 02 Sep 2016, at 13:09, Sun Iba  wrote:
> 
> Hello dear users
> 
> I am following Justin's tutorial for free energy calculation of Methane in
> water. I have downloaded the job.sh file and trying to run it in terminal
> using: sh job.sh but it is giving following error:
> 
> Program mdrun, VERSION 5.0
> Source code file:
> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
> 
> Can not open file:
> min0.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Please help me with error.
> -- 
> 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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Re: [gmx-users] free energy calculation on amino acid mutation

[Mark Abraham]

Hi,

I understand pmx is built exactly for this task.

Mark

On Thu, 26 May 2016 19:35  wrote:

> That really depends on how you approach the problem.
>
> When you choose a dual topology approach you would need to decide where to
> branch off but basically end up with duplicating parts of the residue.
> Sounds like that's what you were trying to do.
>
> In the single topology approach you would match as many atoms as possible
> and balance just the missing atoms with dummies (as opposed to the dual
> approach where you may have lots of them).  As the bonded network stays the
> same you would not need to make any modifications to those.  I do not see
> any reason why you would not want to use this approach in your specific
> case (LEU->GLY).
>
> There is a tool out there that you should probably give a try: pmx.  I
> believe it uses the single topology approach.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Yi An [
> anyiphys...@gmail.com]
> Sent: 26 May 2016 17:44
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] free energy calculation on amino acid mutation
>
> Hi Gromacs users,
>
> I'm trying to calculate the relative binding free energy of a certain
> ligand when a leucine in the ligand binding site is mutated to glycine. The
> concept is simple but I have met some difficulties creating topology files
> for free energy calculation. I have two questions I wish you guys can help:
>
> 1. Let's say my protein have 200 residues and the leucine I want to mutate
> is in the middle (80 for example). When I tried to edit the topology of
> this protein, I found that since the number of atoms changed, I need to
> make lots of changes for bond, angle, and dihedral parameters. Is my
> feeling correct?
>
> 2. If my understanding is correct, I wish there are some existing scripts
> which can help people create topology file for mutational free energy
> calculation. I will highly appreciate if you guys tell me where I can find
> them.
>
> Thank you very much.
>
>
> Yi An
> Postdoctoral Research Associate
> UNC-Chapel Hill
> --
> 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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Re: [gmx-users] free energy calculation on amino acid mutation

[hannes.loeffler]

That really depends on how you approach the problem.

When you choose a dual topology approach you would need to decide where to 
branch off but basically end up with duplicating parts of the residue.  Sounds 
like that's what you were trying to do.

In the single topology approach you would match as many atoms as possible and 
balance just the missing atoms with dummies (as opposed to the dual approach 
where you may have lots of them).  As the bonded network stays the same you 
would not need to make any modifications to those.  I do not see any reason why 
you would not want to use this approach in your specific case (LEU->GLY).

There is a tool out there that you should probably give a try: pmx.  I believe 
it uses the single topology approach.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Yi An 
[anyiphys...@gmail.com]
Sent: 26 May 2016 17:44
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] free energy calculation on amino acid mutation

Hi Gromacs users,

I'm trying to calculate the relative binding free energy of a certain
ligand when a leucine in the ligand binding site is mutated to glycine. The
concept is simple but I have met some difficulties creating topology files
for free energy calculation. I have two questions I wish you guys can help:

1. Let's say my protein have 200 residues and the leucine I want to mutate
is in the middle (80 for example). When I tried to edit the topology of
this protein, I found that since the number of atoms changed, I need to
make lots of changes for bond, angle, and dihedral parameters. Is my
feeling correct?

2. If my understanding is correct, I wish there are some existing scripts
which can help people create topology file for mutational free energy
calculation. I will highly appreciate if you guys tell me where I can find
them.

Thank you very much.


Yi An
Postdoctoral Research Associate
UNC-Chapel Hill
--
Gromacs Users mailing list

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Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Atsutoshi Okabe]

Thanks, Justin.
I uploaded .tpr files that runs on one core(no error) and multiple cores(error 
occurred) below.
http://redmine.gromacs.org/issues/1820
I hope that you give me any comments about  that problem.

Bests,
Atsutoshi

2015/09/03 23:00、Justin Lemkul  のメール：

> 
> 
> On 9/3/15 9:14 AM, Atsutoshi Okabe wrote:
>> Thanks, Justin.
>> I tried turning [bonds],  [angles], [dihedrals] interaction on one-by-one.
>> However, same errors occurred in all cases.
>> Also, I tried the calculation on 1 cpu using the following command and the 
>> error did not occur!
>> (that means I did not use parallelization)
>> gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu
>> 
> 
> Well, here you're invoking an MPI-enabled mdrun without specifying a core 
> count (-nt) so please make sure (from the .log file) that you are, in fact, 
> only using one core.
> 
>> So, I am wondering if the calculation using both 
>> [intermolecular-interactions] tool and parallelization can not work and that 
>> causes the error messages below.
>> [mpiexec@leon304] HYDT_bscu_wait_for_completion 
>> (./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
>> badly; aborting
>> [mpiexec@leon304] HYDT_bsci_wait_for_completion 
>> (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error 
>> waiting for completion
>> [mpiexec@leon304] HYD_pmci_wait_for_completion 
>> (./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting 
>> for completion
>> [mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
>> waiting for completion
>> 
>> I used the following command for parallelization
>> mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus
>> 
> 
> Sounds buggy, but I routinely run my calculations with intermolecular 
> interactions over 32 cores, so it's not inherently a parallelization problem. 
> Could be something unique to your setup.  Please file a bug report 
> onredmine.gromacs.org with this information and provide a .tpr file of a 
> system that runs on one core but fails in parallel.
> 
> -Justin
> 
>> 
>> Bests,
>> Atsutoshi
>> 
>> 2015/09/03 5:42、Justin Lemkul  のメール：
>> 
>>> 
>>> 
>>> On 9/2/15 10:21 AM, Atsutoshi Okabe wrote:
 I mean that the entire [intermolecular_interaction] directive were 
 commented out below;
 ;[ intermolecular-interactions ]
 
>> I tried turning [bonds] or [angles] or [dihedrals] interaction on one-by-one.
>> However, same errors occurred in all cases.
>> Then, I tried the calculation on 1cpu using the following command and the 
>> error did not occur!
>> (that means I do not use parallelization)
>> gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu
>> 
>> So, I am wondering if the calculation using both 
>> [intermolecular-interactions] tool and parallelization can not work and that 
>> causes the error messages.
>> [mpiexec@leon304] HYDT_bscu_wait_for_completion 
>> (./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
>> badly; aborting
>> [mpiexec@leon304] HYDT_bsci_wait_for_completion 
>> (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error 
>> waiting for completion
>> [mpiexec@leon304] HYD_pmci_wait_for_completion 
>> (./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting 
>> for completion
>> [mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
>> waiting for completion
>> 
>> I use the following command to use parallelization
>> mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus
>>> 
 ;[ bonds ]
 ;411 3173  6  0.55  2090
 
 ;[ angles ]
 ;411 3173 3152  1  164.5  20.9
 ;409 411 3173  1  122.3  20.9
 
 ;[ dihedrals ]
 ;409 411 3173 3152  2  12.0  20.9
 ;407 409 411 3173  2  75.6  20.9
 ;411 3173 3152 3144  2  -126.0  20.9
 
 I checked global atom number in .gro file of protein-ligand complex. It 
 looks no problem.
 (407, 409 and 411 are atom number of protein,  3172, 3144 and 3152 are 
 atom number of ligand in gro file of complex)
 Curiously, this error occurs when the vdW interaction between ligand and 
 the environment becomes to turn-off(it means Lambda=0.7~1.0).
 Conversely, the calculations were finished normally when the vdW 
 interaction remains(it means Lambda=0.0~0.7).
 
>>> 
>>> I've never tried using [bonds] in this context; the pull code is a better 
>>> approach.
>>> 
>>> Perhaps there's an issue with the negative dihedral?  Have you tried 
>>> turning these interactions on one-by-one to see if there is a specific 
>>> entry that leads to a failure?  That's the most surefire way to find it.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> 
>>> jale

Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Justin Lemkul]

On 9/3/15 9:14 AM, Atsutoshi Okabe wrote:

Thanks, Justin.
I tried turning [bonds],  [angles], [dihedrals] interaction on one-by-one.
However, same errors occurred in all cases.
Also, I tried the calculation on 1 cpu using the following command and the 
error did not occur!
(that means I did not use parallelization)
gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu



Well, here you're invoking an MPI-enabled mdrun without specifying a core count 
(-nt) so please make sure (from the .log file) that you are, in fact, only using 
one core.



So, I am wondering if the calculation using both [intermolecular-interactions] 
tool and parallelization can not work and that causes the error messages below.
[mpiexec@leon304] HYDT_bscu_wait_for_completion 
(./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
badly; aborting
[mpiexec@leon304] HYDT_bsci_wait_for_completion 
(./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting 
for completion
[mpiexec@leon304] HYD_pmci_wait_for_completion 
(./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for 
completion
[mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
waiting for completion

I used the following command for parallelization
mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus



Sounds buggy, but I routinely run my calculations with intermolecular 
interactions over 32 cores, so it's not inherently a parallelization problem. 
Could be something unique to your setup.  Please file a bug report on 
redmine.gromacs.org with this information and provide a .tpr file of a system 
that runs on one core but fails in parallel.


-Justin



Bests,
Atsutoshi

2015/09/03 5:42、Justin Lemkul  のメール：




On 9/2/15 10:21 AM, Atsutoshi Okabe wrote:

I mean that the entire [intermolecular_interaction] directive were commented 
out below;
;[ intermolecular-interactions ]


I tried turning [bonds] or [angles] or [dihedrals] interaction on one-by-one.
However, same errors occurred in all cases.
Then, I tried the calculation on 1cpu using the following command and the error 
did not occur!
(that means I do not use parallelization)
gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu

So, I am wondering if the calculation using both [intermolecular-interactions] 
tool and parallelization can not work and that causes the error messages.
[mpiexec@leon304] HYDT_bscu_wait_for_completion 
(./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
badly; aborting
[mpiexec@leon304] HYDT_bsci_wait_for_completion 
(./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting 
for completion
[mpiexec@leon304] HYD_pmci_wait_for_completion 
(./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for 
completion
[mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
waiting for completion

I use the following command to use parallelization
mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus



;[ bonds ]
;411 3173  6  0.55  2090

;[ angles ]
;411 3173 3152  1  164.5  20.9
;409 411 3173  1  122.3  20.9

;[ dihedrals ]
;409 411 3173 3152  2  12.0  20.9
;407 409 411 3173  2  75.6  20.9
;411 3173 3152 3144  2  -126.0  20.9

I checked global atom number in .gro file of protein-ligand complex. It looks 
no problem.
(407, 409 and 411 are atom number of protein,  3172, 3144 and 3152 are atom 
number of ligand in gro file of complex)
Curiously, this error occurs when the vdW interaction between ligand and the 
environment becomes to turn-off(it means Lambda=0.7~1.0).
Conversely, the calculations were finished normally when the vdW interaction 
remains(it means Lambda=0.0~0.7).



I've never tried using [bonds] in this context; the pull code is a better 
approach.

Perhaps there's an issue with the negative dihedral?  Have you tried turning 
these interactions on one-by-one to see if there is a specific entry that leads 
to a failure?  That's the most surefire way to find it.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Scie

Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Atsutoshi Okabe]

Thanks, Justin.
I tried turning [bonds],  [angles], [dihedrals] interaction on one-by-one. 
However, same errors occurred in all cases.
Also, I tried the calculation on 1 cpu using the following command and the 
error did not occur!
(that means I did not use parallelization)
gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu

So, I am wondering if the calculation using both [intermolecular-interactions] 
tool and parallelization can not work and that causes the error messages below.
[mpiexec@leon304] HYDT_bscu_wait_for_completion 
(./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
badly; aborting
[mpiexec@leon304] HYDT_bsci_wait_for_completion 
(./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting 
for completion
[mpiexec@leon304] HYD_pmci_wait_for_completion 
(./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for 
completion
[mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
waiting for completion

I used the following command for parallelization
mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus


Bests,
Atsutoshi

2015/09/03 5:42、Justin Lemkul  のメール：

> 
> 
> On 9/2/15 10:21 AM, Atsutoshi Okabe wrote:
>> I mean that the entire [intermolecular_interaction] directive were commented 
>> out below;
>> ;[ intermolecular-interactions ]
>> 
I tried turning [bonds] or [angles] or [dihedrals] interaction on one-by-one. 
However, same errors occurred in all cases.
Then, I tried the calculation on 1cpu using the following command and the error 
did not occur!
(that means I do not use parallelization)
gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu

So, I am wondering if the calculation using both [intermolecular-interactions] 
tool and parallelization can not work and that causes the error messages.
[mpiexec@leon304] HYDT_bscu_wait_for_completion 
(./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
badly; aborting
[mpiexec@leon304] HYDT_bsci_wait_for_completion 
(./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting 
for completion
[mpiexec@leon304] HYD_pmci_wait_for_completion 
(./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for 
completion
[mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
waiting for completion

I use the following command to use parallelization
mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus
> 
>> ;[ bonds ]
>> ;411 3173  6  0.55  2090
>> 
>> ;[ angles ]
>> ;411 3173 3152  1  164.5  20.9
>> ;409 411 3173  1  122.3  20.9
>> 
>> ;[ dihedrals ]
>> ;409 411 3173 3152  2  12.0  20.9
>> ;407 409 411 3173  2  75.6  20.9
>> ;411 3173 3152 3144  2  -126.0  20.9
>> 
>> I checked global atom number in .gro file of protein-ligand complex. It 
>> looks no problem.
>> (407, 409 and 411 are atom number of protein,  3172, 3144 and 3152 are atom 
>> number of ligand in gro file of complex)
>> Curiously, this error occurs when the vdW interaction between ligand and the 
>> environment becomes to turn-off(it means Lambda=0.7~1.0).
>> Conversely, the calculations were finished normally when the vdW interaction 
>> remains(it means Lambda=0.0~0.7).
>> 
> 
> I've never tried using [bonds] in this context; the pull code is a better 
> approach.
> 
> Perhaps there's an issue with the negative dihedral?  Have you tried turning 
> these interactions on one-by-one to see if there is a specific entry that 
> leads to a failure?  That's the most surefire way to find it.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
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> mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Justin Lemkul]

On 9/2/15 10:21 AM, Atsutoshi Okabe wrote:

I mean that the entire [intermolecular_interaction] directive were commented 
out below;
;[ intermolecular-interactions ]

;[ bonds ]
;411 3173  6  0.55  2090

;[ angles ]
;411 3173 3152  1  164.5  20.9
;409 411 3173  1  122.3  20.9

;[ dihedrals ]
;409 411 3173 3152  2  12.0  20.9
;407 409 411 3173  2  75.6  20.9
;411 3173 3152 3144  2  -126.0  20.9

I checked global atom number in .gro file of protein-ligand complex. It looks 
no problem.
(407, 409 and 411 are atom number of protein,  3172, 3144 and 3152 are atom 
number of ligand in gro file of complex)
Curiously, this error occurs when the vdW interaction between ligand and the 
environment becomes to turn-off(it means Lambda=0.7~1.0).
Conversely, the calculations were finished normally when the vdW interaction 
remains(it means Lambda=0.0~0.7).



I've never tried using [bonds] in this context; the pull code is a better 
approach.

Perhaps there's an issue with the negative dihedral?  Have you tried turning 
these interactions on one-by-one to see if there is a specific entry that leads 
to a failure?  That's the most surefire way to find it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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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Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Atsutoshi Okabe]

I mean that the entire [intermolecular_interaction] directive were commented 
out below;
;[ intermolecular-interactions ]

;[ bonds ]
;411 3173  6  0.55  2090

;[ angles ]
;411 3173 3152  1  164.5  20.9
;409 411 3173  1  122.3  20.9

;[ dihedrals ]
;409 411 3173 3152  2  12.0  20.9
;407 409 411 3173  2  75.6  20.9
;411 3173 3152 3144  2  -126.0  20.9

I checked global atom number in .gro file of protein-ligand complex. It looks 
no problem.
(407, 409 and 411 are atom number of protein,  3172, 3144 and 3152 are atom 
number of ligand in gro file of complex)
Curiously, this error occurs when the vdW interaction between ligand and the 
environment becomes to turn-off(it means Lambda=0.7~1.0).
Conversely, the calculations were finished normally when the vdW interaction 
remains(it means Lambda=0.0~0.7).


Bests,
Atsutoshi


2015/09/02 6:25、Justin Lemkul  のメール：

> 
> 
> On 9/1/15 10:12 AM, Atsutoshi Okabe wrote:
>> Thanks, Justin.
>> I want to add restraint between protein and receptor using 
>> [intermolecular-interactions] section(not comment out [bonds], [angles] 
>> [dihedrals] lines)in new support tool of GROMACS 5.1.
>> But I got the error below and I don’t know what causes the problem.
>> 
> 
> I understand what you want to do; I tested this code before it was merged so 
> I certainly know how it works :)
> 
> I'm seeking clarification on what you said before:
> 
> You said: "I tried to comment out the lower row involving [ 
> intermolecular-interactions ] in the topology file and confirmed that the 
> calculation was finished normally."
> 
> What does this mean?  The last line *only* or the entire 
> [intermolecular_interactions] directive?  "Lower row" is not clear.
> 
> The simplest check is to make sure your global atom numbers are right; if 
> they aren't then the physics will of course be unsound.
> 
> -Justin
> 
>> Bests,
>> Atsutoshi
>> 
>> 2015/09/01 11:17、Justin Lemkul  のメール：
>> 
>>> 
>>> 
>>> On 8/31/15 11:20 AM, Atsutoshi Okabe wrote:
 Hi all,
 
 I have a question about how to use inter-molecular bonded interaction tool 
 in GROMACS 5.1.
 I want to calculate binding free energy between protein and ligand adding 
 harmonic restraint force to prevent the ligand from leaving the binding 
 site when the native ligand-receptor interaction are turned off.
 
 So, I added [ intermolecular-interactions ] in complex topology file below.
 [ molecules ]
 ; Compoundnmols
 protein1
 CRW3
 ligand 1
 SOL 11266
 CL   5
 
 [ intermolecular-interactions ]
 
 [ bonds ]
 411 3173  6  0.55  2090
 
 [ angles ]
 411 3173 3152  1  164.5  20.9
 409 411 3173  1  122.3  20.9
 
 [ dihedrals ]
 409 411 3173 3152  2  12.0  20.9
 407 409 411 3173  2  75.6  20.9
 411 3173 3152 3144  2  -126.0  20.9
 
 However, I got the following error.
 
 Reading file equil1.00.tpr, VERSION 5.1 (single precision)
 Changing nstlist from 10 to 40, rlist from 1 to 1
 
 Using 8 MPI processes
 Using 1 OpenMP thread per MPI process
 
 Non-default thread affinity set probably by the OpenMP library,
 disabling internal thread affinity
 [proxy:0:0@leon304] HYDT_dmxu_poll_wait_for_event 
 (./tools/demux/demux_poll.c:70): assert (!(pollfds[i].revents & ~POLLIN & 
 ~POLLOUT & ~POLLHUP)) failed
 [proxy:0:0@leon304] main (./pm/pmiserv/pmip.c:387): demux engine error 
 waiting for event
 [mpiexec@leon304] HYDT_bscu_wait_for_completion 
 (./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
 badly; aborting
 [mpiexec@leon304] HYDT_bsci_wait_for_completion 
 (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error 
 waiting for completion
 [mpiexec@leon304] HYD_pmci_wait_for_completion 
 (./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting 
 for completion
 [mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
 waiting for completion
 
 I tried to comment out the lower row involving [ 
 intermolecular-interactions ] in the topology file and confirmed that the 
 calculation was finished normally.
 (Of course, the ligand was leaving from the binding site when the 
 ligand-receptor interaction are completely turned off.)
 Could you advice me how to solve this error?
 
>>> 
>>> You mean when you comment out all of the intermolecular interactions, or 
>>> literally just the last line.  If the latter, then you've found your 
>>> problem.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.

Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Justin Lemkul]

On 9/1/15 10:12 AM, Atsutoshi Okabe wrote:

Thanks, Justin.
I want to add restraint between protein and receptor using 
[intermolecular-interactions] section(not comment out [bonds], [angles] 
[dihedrals] lines)in new support tool of GROMACS 5.1.
But I got the error below and I don’t know what causes the problem.



I understand what you want to do; I tested this code before it was merged so I 
certainly know how it works :)


I'm seeking clarification on what you said before:

You said: "I tried to comment out the lower row involving [ 
intermolecular-interactions ] in the topology file and confirmed that the 
calculation was finished normally."


What does this mean?  The last line *only* or the entire 
[intermolecular_interactions] directive?  "Lower row" is not clear.


The simplest check is to make sure your global atom numbers are right; if they 
aren't then the physics will of course be unsound.


-Justin


Bests,
Atsutoshi

2015/09/01 11:17、Justin Lemkul  のメール：




On 8/31/15 11:20 AM, Atsutoshi Okabe wrote:

Hi all,

I have a question about how to use inter-molecular bonded interaction tool in 
GROMACS 5.1.
I want to calculate binding free energy between protein and ligand adding 
harmonic restraint force to prevent the ligand from leaving the binding site 
when the native ligand-receptor interaction are turned off.

So, I added [ intermolecular-interactions ] in complex topology file below.
[ molecules ]
; Compoundnmols
protein1
CRW3
ligand 1
SOL 11266
CL   5

[ intermolecular-interactions ]

[ bonds ]
411 3173  6  0.55  2090

[ angles ]
411 3173 3152  1  164.5  20.9
409 411 3173  1  122.3  20.9

[ dihedrals ]
409 411 3173 3152  2  12.0  20.9
407 409 411 3173  2  75.6  20.9
411 3173 3152 3144  2  -126.0  20.9

However, I got the following error.

Reading file equil1.00.tpr, VERSION 5.1 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1

Using 8 MPI processes
Using 1 OpenMP thread per MPI process

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
[proxy:0:0@leon304] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:70): assert 
(!(pollfds[i].revents & ~POLLIN & ~POLLOUT & ~POLLHUP)) failed
[proxy:0:0@leon304] main (./pm/pmiserv/pmip.c:387): demux engine error waiting 
for event
[mpiexec@leon304] HYDT_bscu_wait_for_completion 
(./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
badly; aborting
[mpiexec@leon304] HYDT_bsci_wait_for_completion 
(./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting 
for completion
[mpiexec@leon304] HYD_pmci_wait_for_completion 
(./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for 
completion
[mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
waiting for completion

I tried to comment out the lower row involving [ intermolecular-interactions ] 
in the topology file and confirmed that the calculation was finished normally.
(Of course, the ligand was leaving from the binding site when the 
ligand-receptor interaction are completely turned off.)
Could you advice me how to solve this error?



You mean when you comment out all of the intermolecular interactions, or 
literally just the last line.  If the latter, then you've found your problem.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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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mail to gmx-users-requ...@gromacs.org.




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Atsutoshi Okabe]

Thanks, Justin.
I want to add restraint between protein and receptor using 
[intermolecular-interactions] section(not comment out [bonds], [angles] 
[dihedrals] lines)in new support tool of GROMACS 5.1.
But I got the error below and I don’t know what causes the problem.

Bests,
Atsutoshi

2015/09/01 11:17、Justin Lemkul  のメール：

> 
> 
> On 8/31/15 11:20 AM, Atsutoshi Okabe wrote:
>> Hi all,
>> 
>> I have a question about how to use inter-molecular bonded interaction tool 
>> in GROMACS 5.1.
>> I want to calculate binding free energy between protein and ligand adding 
>> harmonic restraint force to prevent the ligand from leaving the binding site 
>> when the native ligand-receptor interaction are turned off.
>> 
>> So, I added [ intermolecular-interactions ] in complex topology file below.
>> [ molecules ]
>> ; Compoundnmols
>> protein1
>> CRW3
>> ligand 1
>> SOL 11266
>> CL   5
>> 
>> [ intermolecular-interactions ]
>> 
>> [ bonds ]
>> 411 3173  6  0.55  2090
>> 
>> [ angles ]
>> 411 3173 3152  1  164.5  20.9
>> 409 411 3173  1  122.3  20.9
>> 
>> [ dihedrals ]
>> 409 411 3173 3152  2  12.0  20.9
>> 407 409 411 3173  2  75.6  20.9
>> 411 3173 3152 3144  2  -126.0  20.9
>> 
>> However, I got the following error.
>> 
>> Reading file equil1.00.tpr, VERSION 5.1 (single precision)
>> Changing nstlist from 10 to 40, rlist from 1 to 1
>> 
>> Using 8 MPI processes
>> Using 1 OpenMP thread per MPI process
>> 
>> Non-default thread affinity set probably by the OpenMP library,
>> disabling internal thread affinity
>> [proxy:0:0@leon304] HYDT_dmxu_poll_wait_for_event 
>> (./tools/demux/demux_poll.c:70): assert (!(pollfds[i].revents & ~POLLIN & 
>> ~POLLOUT & ~POLLHUP)) failed
>> [proxy:0:0@leon304] main (./pm/pmiserv/pmip.c:387): demux engine error 
>> waiting for event
>> [mpiexec@leon304] HYDT_bscu_wait_for_completion 
>> (./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
>> badly; aborting
>> [mpiexec@leon304] HYDT_bsci_wait_for_completion 
>> (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error 
>> waiting for completion
>> [mpiexec@leon304] HYD_pmci_wait_for_completion 
>> (./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting 
>> for completion
>> [mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
>> waiting for completion
>> 
>> I tried to comment out the lower row involving [ intermolecular-interactions 
>> ] in the topology file and confirmed that the calculation was finished 
>> normally.
>> (Of course, the ligand was leaving from the binding site when the 
>> ligand-receptor interaction are completely turned off.)
>> Could you advice me how to solve this error?
>> 
> 
> You mean when you comment out all of the intermolecular interactions, or 
> literally just the last line.  If the latter, then you've found your problem.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

[Justin Lemkul]

On 8/31/15 11:20 AM, Atsutoshi Okabe wrote:

Hi all,

I have a question about how to use inter-molecular bonded interaction tool in 
GROMACS 5.1.
I want to calculate binding free energy between protein and ligand adding 
harmonic restraint force to prevent the ligand from leaving the binding site 
when the native ligand-receptor interaction are turned off.

So, I added [ intermolecular-interactions ] in complex topology file below.
[ molecules ]
; Compoundnmols
protein1
CRW3
ligand 1
SOL 11266
CL   5

[ intermolecular-interactions ]

[ bonds ]
411 3173  6  0.55  2090

[ angles ]
411 3173 3152  1  164.5  20.9
409 411 3173  1  122.3  20.9

[ dihedrals ]
409 411 3173 3152  2  12.0  20.9
407 409 411 3173  2  75.6  20.9
411 3173 3152 3144  2  -126.0  20.9

However, I got the following error.

Reading file equil1.00.tpr, VERSION 5.1 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1

Using 8 MPI processes
Using 1 OpenMP thread per MPI process

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
[proxy:0:0@leon304] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:70): assert 
(!(pollfds[i].revents & ~POLLIN & ~POLLOUT & ~POLLHUP)) failed
[proxy:0:0@leon304] main (./pm/pmiserv/pmip.c:387): demux engine error waiting 
for event
[mpiexec@leon304] HYDT_bscu_wait_for_completion 
(./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated 
badly; aborting
[mpiexec@leon304] HYDT_bsci_wait_for_completion 
(./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting 
for completion
[mpiexec@leon304] HYD_pmci_wait_for_completion 
(./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for 
completion
[mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error 
waiting for completion

I tried to comment out the lower row involving [ intermolecular-interactions ] 
in the topology file and confirmed that the calculation was finished normally.
(Of course, the ligand was leaving from the binding site when the 
ligand-receptor interaction are completely turned off.)
Could you advice me how to solve this error?



You mean when you comment out all of the intermolecular interactions, or 
literally just the last line.  If the latter, then you've found your problem.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Free energy calculation for aminoacids

[Justin Lemkul]

On 6/27/15 8:48 AM, Marzieh Saeedi Masineh wrote:

Hi all
I want to calculate free energy of solvation  for a leucine and some other 
aminoacids individually,according to Justin tutorial : methane in the water.
Is it reasonable to follow that  method  for free energy determination of one 
amino acid?



Yes, provided you also do the charge transformation.  The methane example is 
clearly defined as a van der Waals transformation; that is not a full hydration 
free energy.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation

[Justin Lemkul]

On 6/22/15 7:10 AM, nazli kashani javid wrote:

thanks for your clear answer.

Is there any reasonable method for calculating free energy of solvation for
my protein? :-(



Try MM/PBSA or MM/GBSA calculations.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation

[nazli kashani javid]

I'm trying to show thermodynamic stabilities of my protein from free energy
simulation. And I chose free energy of solvation, so if I can't use this
method how can I show thermodynamic stabilities of my protein?



On Mon, Jun 22, 2015 at 3:40 PM, nazli kashani javid 
wrote:

> thanks for your clear answer.
>
> Is there any reasonable method for calculating free energy of solvation
> for my protein? :-(
>
>
>
>
>
> On Mon, Jun 22, 2015 at 2:26 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 6/22/15 5:53 AM, nazli kashani javid wrote:
>>
>>> Dear all
>>>
>>> I'm trying to calculate free energy of solvation according to Justin's
>>> tutorial for my protein in water.
>>>
>>> Is it true to follow that tutorial for my protein? any special changes in
>>> MDP file is necessary ?
>>>
>>>
>> You shouldn't use this method at all for a protein; the calculations will
>> never converge.
>>
>>  If there is no differences for systems to calculate free energy of
>>> solvation according to Justin's tutorial. I have set all my residue's
>>> charges to zero. and there is no ions into my solvent.
>>>
>>>
>> Don't do this.  The tutorial uses zero charges on methane because its
>> stated purpose is to calculate *only* the vdW contribution to the free
>> energy of solvation, and (as the tutorial says) it assumes the charges have
>> already been scaled to zero, which is necessary for the full free energy of
>> solvation.
>>
>> Regardless, you shouldn't do this kind of calculation on a full protein.
>>
>> -Justin
>>
>>  I received this error several times during minimization (em_steep). Even
>>> when I change  some parameters in .mdp file such as pme_order or rvdw or
>>> vdw-type  and , the error didn't change.
>>>
>>>
>>> Fatal error:
>>> There is no domain decomposition for 10 nodes that is compatible with the
>>> given box and a minimum cell size of 4.2267 nm
>>> Change the number of nodes or mdrun option -rdd
>>> Look in the log file for details on the domain decomposition
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>> I checked the website but I didn't get any helpful hint for my system.
>>>
>>> any help is appreciated.
>>>
>>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> 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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Re: [gmx-users] Free energy calculation

[nazli kashani javid]

thanks for your clear answer.

Is there any reasonable method for calculating free energy of solvation for
my protein? :-(





On Mon, Jun 22, 2015 at 2:26 PM, Justin Lemkul  wrote:

>
>
> On 6/22/15 5:53 AM, nazli kashani javid wrote:
>
>> Dear all
>>
>> I'm trying to calculate free energy of solvation according to Justin's
>> tutorial for my protein in water.
>>
>> Is it true to follow that tutorial for my protein? any special changes in
>> MDP file is necessary ?
>>
>>
> You shouldn't use this method at all for a protein; the calculations will
> never converge.
>
>  If there is no differences for systems to calculate free energy of
>> solvation according to Justin's tutorial. I have set all my residue's
>> charges to zero. and there is no ions into my solvent.
>>
>>
> Don't do this.  The tutorial uses zero charges on methane because its
> stated purpose is to calculate *only* the vdW contribution to the free
> energy of solvation, and (as the tutorial says) it assumes the charges have
> already been scaled to zero, which is necessary for the full free energy of
> solvation.
>
> Regardless, you shouldn't do this kind of calculation on a full protein.
>
> -Justin
>
>  I received this error several times during minimization (em_steep). Even
>> when I change  some parameters in .mdp file such as pme_order or rvdw or
>> vdw-type  and , the error didn't change.
>>
>>
>> Fatal error:
>> There is no domain decomposition for 10 nodes that is compatible with the
>> given box and a minimum cell size of 4.2267 nm
>> Change the number of nodes or mdrun option -rdd
>> Look in the log file for details on the domain decomposition
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> I checked the website but I didn't get any helpful hint for my system.
>>
>> any help is appreciated.
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Free energy calculation

[Justin Lemkul]

On 6/22/15 5:53 AM, nazli kashani javid wrote:

Dear all

I'm trying to calculate free energy of solvation according to Justin's
tutorial for my protein in water.

Is it true to follow that tutorial for my protein? any special changes in
MDP file is necessary ?



You shouldn't use this method at all for a protein; the calculations will never 
converge.



If there is no differences for systems to calculate free energy of
solvation according to Justin's tutorial. I have set all my residue's
charges to zero. and there is no ions into my solvent.



Don't do this.  The tutorial uses zero charges on methane because its stated 
purpose is to calculate *only* the vdW contribution to the free energy of 
solvation, and (as the tutorial says) it assumes the charges have already been 
scaled to zero, which is necessary for the full free energy of solvation.


Regardless, you shouldn't do this kind of calculation on a full protein.

-Justin


I received this error several times during minimization (em_steep). Even
when I change  some parameters in .mdp file such as pme_order or rvdw or
vdw-type  and , the error didn't change.


Fatal error:
There is no domain decomposition for 10 nodes that is compatible with the
given box and a minimum cell size of 4.2267 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I checked the website but I didn't get any helpful hint for my system.

any help is appreciated.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT (Justin Lemkul)

[Jin Zhang]

Dear Justin,

We thought about this, and checked these non-crashed lambda tpr as well as
the pre-equilbrated NPT step, all showed mismatch between posre-com[0]
posre-com[1] posre-com[2], and the real com. So I suspect this posre-com is
not the real center of mass for NPT simulation.
Since the reference coordinate is read from -c .gro when perform grompp, it
should not be wrong, unless it read elsewhere.

Best,
Jin


> Date: Wed, 18 Feb 2015 07:42:30 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] free energy calculation: combination of
> position restraint +refcoord_scaling cause crash during NPT
> Message-ID: <54e488b6.9090...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/17/15 12:31 PM, Jin Zhang wrote:
> > Dear all,
> >
> > We're doing free energy calculation and found some of my lambda job
> crashes
> > due to the combination of position restraint +refcoord_scaling COM. All
> > crashes happened at NPT steps.
> >
> > By checking each energy term, we found the Position Rest. term is
> > surprisingly as high as 10^6 kJ/mol, the others look fine. Either turn of
> > position restrain or refcoord_scaling could avoid the simulation to be
> > crashed. We tried to see if there's mismatch of either COM or coordinate
> > and found no direct answer.
> > Any help would be appreciated!
> >
> > In the tpr file
> >refcoord-scaling = COM
> >posres-com (3):
> >posres-com[0]= 3.15034e-01
> >posres-com[1]= 4.48110e-01
> >posres-com[2]= 5.17730e-01
> >
> > COM of protein-ligand calculated by t_traj -com -ox
> > 3.024224.301694.84964
> >
>
> If the reference COM is defined as (0.315,0.448,0.518) and your actual
> coordinates are what you're shown above, there will inherently be a huge
> restraint potential as mdrun tries to bias the coordinates towards the
> defined
> reference.  I suspect something is wrong in your definition of your
> reference.
>
> -Justin
>
> > coordinate of 1st atom in tpr: posres_xA[0]={ 1.39783e-01,
> > -9.56922e-02,  1.22536e+00}
> > coordinate of 1st atom in gro: 1MOL C11   3.164   4.206
> > 6.075
> >
> > The same thing was also found in a normal non-free energy simulations
> with
> > combination of position restrain and refcoord-scaling.
> > Later on, we found some other people also have the same problem when use
> > that combination to do free energy calculation.
> > http://comments.gmane.org/gmane.science.biology.gromacs.user/66177
> > It makes more sense to me to turn on refcoord_scaling while using
> position
> > restraint.
> > Again, any help to understand this would be appreciated!
> >
> > Regards,
> > Jin
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
>
> --
>
> Message: 3
> Date: Wed, 18 Feb 2015 19:48:50 +0530
> From: Sanchaita Rajkhowa 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] simulation of heme along with h2o2
> Message-ID:
>  nrjnyajn8uwmmwysvsr4x...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all, I am trying to simulate a heme containing protein in high
> concentration (having hydrogen peroxide). However, I do not know which
> forcefield to use. Heme has forcefield in gromos96 but not the forcefield
> of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
> help.
>
> Thanks in advance.
> Sanchaita.
>
>
> --
>
> Message: 4
> Date: Wed, 18 Feb 2015 16:30:34 +0100
> From: "Carmen Di Giovanni" 
> To: 
> Subject: [gmx-users] GPU low performance
> Message-ID: <8525B4BE52BB4609BCED7556FAFB3587@PCCarmen>
> Content-Type: text/plain;   charset="iso-8859-1"
>
> Daear all,
> I'm working on a machine with an INVIDIA Teska K20.
> After a minimization on a protein of 1925 atoms this is the mesage:
>
> Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
> For optimal performance this ratio should be close to 1!
>
>
> NOTE: The GPU has >25% less

Re: [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT

[Justin Lemkul]

On 2/17/15 12:31 PM, Jin Zhang wrote:

Dear all,

We're doing free energy calculation and found some of my lambda job crashes
due to the combination of position restraint +refcoord_scaling COM. All
crashes happened at NPT steps.

By checking each energy term, we found the Position Rest. term is
surprisingly as high as 10^6 kJ/mol, the others look fine. Either turn of
position restrain or refcoord_scaling could avoid the simulation to be
crashed. We tried to see if there's mismatch of either COM or coordinate
and found no direct answer.
Any help would be appreciated!

In the tpr file
   refcoord-scaling = COM
   posres-com (3):
   posres-com[0]= 3.15034e-01
   posres-com[1]= 4.48110e-01
   posres-com[2]= 5.17730e-01

COM of protein-ligand calculated by t_traj -com -ox
3.024224.301694.84964



If the reference COM is defined as (0.315,0.448,0.518) and your actual 
coordinates are what you're shown above, there will inherently be a huge 
restraint potential as mdrun tries to bias the coordinates towards the defined 
reference.  I suspect something is wrong in your definition of your reference.


-Justin


coordinate of 1st atom in tpr: posres_xA[0]={ 1.39783e-01,
-9.56922e-02,  1.22536e+00}
coordinate of 1st atom in gro: 1MOL C11   3.164   4.206
6.075

The same thing was also found in a normal non-free energy simulations with
combination of position restrain and refcoord-scaling.
Later on, we found some other people also have the same problem when use
that combination to do free energy calculation.
http://comments.gmane.org/gmane.science.biology.gromacs.user/66177
It makes more sense to me to turn on refcoord_scaling while using position
restraint.
Again, any help to understand this would be appreciated!

Regards,
Jin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation by MM_PBSA

[Indu Kumari]

Hello everyone,

I tried to do it for single (snapshot) .trr file, but the error is same,
SEGMENTATION FAULT. I am not able to figure out problem.

With regards,
Indu

On Tue, Dec 9, 2014 at 1:56 PM, Indu Kumari  wrote:
>
> Thank you.
>
>
> With regards,
> Indu
>
> On Tue, Dec 9, 2014 at 12:59 PM, Bikash Ranjan Sahoo <
> bikash.bioinformat...@gmail.com> wrote:
>
>> Hi,
>> This usually occurred when you run apbs for a large number of
>> conformations
>> serially. Sometimes, a big protein (800-1000 residues) also arrested the
>> program as apbs consumes a very high memory on cluster (in my case for 500
>> snapshots ~400 aa long protein it consumes ~300-400GB). Try using a small
>> number of snapshots if you are running in parallel. And if you are running
>> one pro, lig and complex in your local computer, kindly check the CPU
>> usage
>> and do the needful. Core dumped usually  fired with memory inadequacy.
>>
>> --
>> *BIKASH RANJAN SAHOO *
>>
>> *​Osaka Univ. Japan​*
>>
>> On Tue, Dec 9, 2014 at 4:16 PM, Indu Kumari 
>> wrote:
>>
>> > Hello everyone,
>> >
>> > I am trying to calculate free energy of protein ligand complex by using
>> > MM_PBSA method. While calculating polar solvation energy of the
>> complex, I
>> > am getting this error.
>> >
>> > * Segmentation fault (core dumped).*
>> >
>> > *Please help!*
>> > With regards,
>> > Indu
>> > --
>> > 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.
>> >
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] Free energy calculation by MM_PBSA

[Indu Kumari]

Thank you.


With regards,
Indu

On Tue, Dec 9, 2014 at 12:59 PM, Bikash Ranjan Sahoo <
bikash.bioinformat...@gmail.com> wrote:

> Hi,
> This usually occurred when you run apbs for a large number of conformations
> serially. Sometimes, a big protein (800-1000 residues) also arrested the
> program as apbs consumes a very high memory on cluster (in my case for 500
> snapshots ~400 aa long protein it consumes ~300-400GB). Try using a small
> number of snapshots if you are running in parallel. And if you are running
> one pro, lig and complex in your local computer, kindly check the CPU usage
> and do the needful. Core dumped usually  fired with memory inadequacy.
>
> --
> *BIKASH RANJAN SAHOO *
>
> *​Osaka Univ. Japan​*
>
> On Tue, Dec 9, 2014 at 4:16 PM, Indu Kumari 
> wrote:
>
> > Hello everyone,
> >
> > I am trying to calculate free energy of protein ligand complex by using
> > MM_PBSA method. While calculating polar solvation energy of the complex,
> I
> > am getting this error.
> >
> > * Segmentation fault (core dumped).*
> >
> > *Please help!*
> > With regards,
> > Indu
> > --
> > 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.
> >
> --
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Re: [gmx-users] Free energy calculation by MM_PBSA

[Bikash Ranjan Sahoo]

Hi,
This usually occurred when you run apbs for a large number of conformations
serially. Sometimes, a big protein (800-1000 residues) also arrested the
program as apbs consumes a very high memory on cluster (in my case for 500
snapshots ~400 aa long protein it consumes ~300-400GB). Try using a small
number of snapshots if you are running in parallel. And if you are running
one pro, lig and complex in your local computer, kindly check the CPU usage
and do the needful. Core dumped usually  fired with memory inadequacy.

--
*BIKASH RANJAN SAHOO *

*​Osaka Univ. Japan​*

On Tue, Dec 9, 2014 at 4:16 PM, Indu Kumari  wrote:

> Hello everyone,
>
> I am trying to calculate free energy of protein ligand complex by using
> MM_PBSA method. While calculating polar solvation energy of the complex, I
> am getting this error.
>
> * Segmentation fault (core dumped).*
>
> *Please help!*
> With regards,
> Indu
> --
> 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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Re: [gmx-users] Free Energy calculation

[Justin Lemkul]

On 11/18/14 11:46 PM, RINU KHATTRI wrote:

Thank you justin is there any tutorial like kalp in dppc which i can follow
how can i calculate the diffusion coefficient of ligand(drug)
thanks in advance



You can calculate diffusion coefficients with g_msd.

-Justin


On Fri, Nov 14, 2014 at 12:04 AM, Justin Lemkul  wrote:



On 11/13/14 4:09 AM, RINU KHATTRI wrote:


hello gromacs users i am working on protein ligand complex with popc
membrane i want to calculate the free energy of protein and ligand i
have to follow which tutorial (methane in  water) but my protein is
membrane protein i am also running md simulation (70 ns)  i am new in
free energy calculation from where i have to start after the
production md or  i can start from the original pdb file



The "free energy of protein and ligand" is a rather ill-defined quantity.
Are you trying to calculate binding free energy?  If so, there's a huge
amount of literature on this topic.  It comes down to simply doing a
thermodynamic cycle of the ligand in water and in the binding site.
Restraints might be needed to keep the ligand bound while being decoupled,
but again there's tons of papers on this topic.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free Energy calculation

[RINU KHATTRI]

Thank you justin is there any tutorial like kalp in dppc which i can follow
how can i calculate the diffusion coefficient of ligand(drug)
thanks in advance

On Fri, Nov 14, 2014 at 12:04 AM, Justin Lemkul  wrote:
>
>
> On 11/13/14 4:09 AM, RINU KHATTRI wrote:
>>
>> hello gromacs users i am working on protein ligand complex with popc
>> membrane i want to calculate the free energy of protein and ligand i
>> have to follow which tutorial (methane in  water) but my protein is
>> membrane protein i am also running md simulation (70 ns)  i am new in
>> free energy calculation from where i have to start after the
>> production md or  i can start from the original pdb file
>
>
> The "free energy of protein and ligand" is a rather ill-defined quantity.
> Are you trying to calculate binding free energy?  If so, there's a huge
> amount of literature on this topic.  It comes down to simply doing a
> thermodynamic cycle of the ligand in water and in the binding site.
> Restraints might be needed to keep the ligand bound while being decoupled,
> but again there's tons of papers on this topic.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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Re: [gmx-users] Free Energy calculation

[Justin Lemkul]

On 11/13/14 4:09 AM, RINU KHATTRI wrote:

hello gromacs users i am working on protein ligand complex with popc
membrane i want to calculate the free energy of protein and ligand i
have to follow which tutorial (methane in  water) but my protein is
membrane protein i am also running md simulation (70 ns)  i am new in
free energy calculation from where i have to start after the
production md or  i can start from the original pdb file


The "free energy of protein and ligand" is a rather ill-defined quantity.  Are 
you trying to calculate binding free energy?  If so, there's a huge amount of 
literature on this topic.  It comes down to simply doing a thermodynamic cycle 
of the ligand in water and in the binding site.  Restraints might be needed to 
keep the ligand bound while being decoupled, but again there's tons of papers on 
this topic.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] free energy calculation

[Justin Lemkul]

On 10/20/14 6:16 AM, RINU KHATTRI wrote:

hello gromacs users i am working on protein complex with popc membrane
i want to calculate the free energy of complex i have run protein
complex and  dppc tutorial   how to start for that i am using 4.5
version of gromacs should i use

GROMACS Tutorial Free Energy Calculations: Methane in Water

kindly help



Your question is ill-defined.  Free energy of what?  If you're looking for free 
energy of ligand binding, the fact that the protein is in the membrane is of 
little practical difference to any other protein-ligand complex.  Compute a full 
thermodynamic cycle in the binding site, and one in water, and take the difference.


The methane-in-water example is the basic idea, and discusses the process for 
full cycles on ligand systems, but doesn't illustrate it explicitly.  There's 
tons of literature on this topic, though.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] free energy calculation for methane

[Justin Lemkul]

On 10/16/14 9:33 AM, elham tazikeh wrote:

Dear Justin
thanks for your reply

i trying to follow your tutorial but when i want to produce neccesary files
per lambdas by this command:
Perl write_mdp.pl em_steep.mdp
i received 20 files as i expected but they are empty,


No idea.  Works perfectly for me.


for this reason i try to change some important parameters in your mdp file
(we have mdp files for lambda=0) in other lambdas.for instance
*init_lambda_state=0.05
or 0.1 or 0.15 , ...*


The value of init_lambda_state is an integer index, specifying which lambda 
vector is being used.  See the comment line in, e.g., em_steep.mdp for the 
labeling (which is also printed in the tutorial in step 3).



but i dont know what value is instead of *delta_lambda?*



It is not used.  See step 3 of the tutorial where this is explained.


*mdp file for lambda=0*
; Free energy control stuff
free_energy  = yes

**init_lambda_state= 0**delta_lambda = 0**
calc_lambda_neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state012345678
910   11   12   13   14   15   16   17   18   19   20
vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00

also, you mentioned about *foreign_lambda* in your tutorial, but i didnot
see it in mdp files.



Some of the wording in step 7 was an artifact of the old tutorial.  That has 
been fixed for the most part now, but I still probably need to do a bit of 
revising.  The concept of "native" and "foreign" lambda still applies in 
understanding BAR, for which you will have to read the actual Bennett paper.



at the end, i want to know about the differences between *write_mdp.pl
* and *write_sh.pl * and* job.sh*?



One writes the .mdp files, the other writes bash scripts that execute the runs.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] free energy calculation

[Justin Lemkul]

On 10/16/14 5:02 AM, elham tazikeh wrote:

Dear users
For calculating free energy of methan (in justin tutorial)
I changed important parameters instead of  the parameters in lambda=0  that
having in that tutorial
Is it correct?


If you're trying to execute the tutorial, no, don't make any changes.


Or i must create those files by this command:
Perl write_mdp.pl em_steep.mdp for every lambda?!

I did this way.but my received files were empty


The scripts should write all the necessary files.  I don't know why they would 
produce blank output.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Free energy calculation of a charged system

[Valentina]

Hi! Thank you for reply.

You have lost me there, tbh.

I think I didn't make it clear, I have either organic -vely changed molecule
or Cl-. Those counterbalance the +vely charged material. Therefore, I either
have organics or clorine. So, if I do TI and completely decouple vow and
charges:

couple-intramol  = yes   
couple-lambda0   = none
couple-lambda1   = vdwq

but then, obviously, I run into problems when simulating charged system (i.e
it crashes)

so, I am thinking of running:

couple-intramol  = yes   
couple-lambda0   = none
couple-lambda1   = vdw

i.e. keeping the charge to balance and having total charge 0 of the
simulation box.


Then the plan would be:

Org -veTI  -ve charge remains  TI   

Cl -ve
Material +ve   > Material +ve ->  
Material +ve


Does this make sense? Or it is possible to go from Organics to Cl- directly
in one integration sequence?

Thank you for your advises,
V







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Re: [gmx-users] Free energy calculation of a charged system

[Dr. Vitaly Chaban]

Hi Valentina -

Honestly, I did not get the considerations with charges. TI probably
scales interaction energies between selected groups, not charges.

Science-wise, I would first decouple organic particle, then decouple
chloride anions,  and place a right sign between these two free
energies. If you substitute an ion in the neutral system by a
molecule, your system free energy will not definitely like this giving
a positive (delta)G.


Dr. Vitaly V. Chaban


On Fri, Mar 14, 2014 at 4:52 PM, Valentina
 wrote:
> Hello,
>
> I need an advise on how it is better to approach the ThermoD integration of
> such system:
> +vely charged inorganic layer, filled with water and counterbalanced by -ve
> organics
>
> Do I integrate out organics both VdW and Coulomb, making the system have
> total +ve charge at lambda = 1
>
> OR:
>
> Do I integrate out organics only by VdW, leaving Couloumb interactions, by
> such having a neutral system at lambda = 1
>
> I ideally want to compare the free energies of the substituting Cl- ions
> with organic molecules, but I don't think I can just change Cl- at lambda =0
> for an organics at lambda =1 (or can I?) Therefore I was planning to perform
> Thermod integration of both systems independently, also Cl- and organics in
> vacuum (again charges issue) and calculate partition ratios.
>
> Thank you for advise,
> V
>
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> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Free-energy-calculation-of-a-charged-system-tp5015154.html
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Re: [gmx-users] Free energy calculation of multiple solutes

[Justin Lemkul]

On 2/20/14, 1:00 AM, Jeff Chen wrote:

Thank you very much for the quick reply.

Without using tpbconv and mdrun -rerun, I'm not sure how to get the
solute-solute energies from gromacs (please let me know it there's a way to do
this) -- since there are many more solvent molecules, the total potential energy


Nonbonded interactions are decomposed with energygrps.  If you didn't include 
that keyword and proper settings in the original run, then you need to use mdrun 
-rerun, but that doesn't really help for solving this issue.  Investigating 
energygrps while the free energy code is on is worth checking into on its own. 
In principle, it should work, but may simply have never been tested.



is dominated by solvent-solvent and solvent-solute interactions. However, the
total potential energy from a simulation (not a free energy simulation) with the
solute charges set to zero is different than that obtained from a free energy
simulation with lambda=1 -- the differences are fairly small, but big enough to
be worrisome.



Good to know.  What Gromacs version is this?


I'll run a system with fewer solvent molecules to get a better handle on what's
going on -- thanks again for your suggestions.

It seems most people do free energy calculations with a single solute molecule
-- in your opinion, is it very unlikely that there is any problem in the way
solute-solute interactions are handled in the free energy simulations?



That would be a fundamentally serious flaw in the free energy code; I think it 
highly unlikely that something so essential is broken.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Free energy calculation of multiple solutes

[Jeff Chen]

Thank you very much for the quick reply.

Without using tpbconv and mdrun -rerun, I'm not sure how to get the
solute-solute energies from gromacs (please let me know it there's a way to
do this) -- since there are many more solvent molecules, the total
potential energy is dominated by solvent-solvent and solvent-solute
interactions. However, the total potential energy from a simulation (not a
free energy simulation) with the solute charges set to zero is different
than that obtained from a free energy simulation with lambda=1 -- the
differences are fairly small, but big enough to be worrisome.

I'll run a system with fewer solvent molecules to get a better handle on
what's going on -- thanks again for your suggestions.

It seems most people do free energy calculations with a single solute
molecule -- in your opinion, is it very unlikely that there is any problem
in the way solute-solute interactions are handled in the free energy
simulations?

Thanks again,

Jeff


On Wed, Feb 19, 2014 at 7:34 PM, Justin Lemkul  wrote:

>
>
> On 2/19/14, 1:05 PM, Jeff Chen wrote:
>
>> Dear All,
>>
>> I am trying to calculate the change in free energy that occurs when
>> charging multiple type B molecules in an A-B mixture. For example, I have
>> a
>> mixture of 900 molecules of type A and 100 of type B. When coulomb
>> interactions are on, B is identical to A (something like TIP4P water), but
>> when coulomb interactions are off, each B is simply a Lennard-Jones
>> particle (in the topology file, I've labelled B differently and called the
>> molecule SOLB, but all interaction information is identical to A). To do
>> the free energy calculations, I perform different simulations at each
>> lambda point. For example, for a simulation with lambda=0, I have the
>> following in my .mdp file:
>>
>> free_energy = yes
>> init_lambda = 0.0
>> delta_lambda = 0
>> foreign_lambda= 0.05
>> couple-lambda0=vdw-q
>> couple-lambda1=vdw
>> couple-moltype=SOLB
>>
>> and when lamba=1,
>>
>> free_energy = yes
>> init_lambda = 1.0
>> delta_lambda = 0
>> foreign_lambda= 0.95
>> couple-lambda0=vdw-q
>> couple-lambda1=vdw
>> couple-moltype=SOLB
>>
>> I expected that when lambda=0, B molecules would behave identically to A
>> molecules with the coulombic energy fully turned on
>> (couple-lambda0=vdw-q),
>> and when lambda=1, B molecules would behave like LJ particles, with no
>> coulombic interactions, either with each other, or with A molecules.
>>
>> However, when I look at the coulombic energy for B-B interactions (I used
>> tpbconv -o to make a new *.tpr for only B molecules, then used mdrun
>> -rerun
>> with a trajectory containing only information about B molecules), I find
>> that both the short-range and reciprocal coulombic energies are NOT zero
>> as
>> I had expected for lambda = 1, and are in fact exactly equal to the
>> negative of the respective coulombic energies obtained using the same
>> trajectory data when lambda=0.
>>
>
> What are the energies without using tpbconv and mdrun -rerun?  In other
> words, it's necessary to figure out whether this is a problem in the
> original simulation with the free energy code (unlikely, given how simple
> the system is) or a problem using mdrun -rerun in conjunction with the free
> energy code (far more likely).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Free energy calculation of multiple solutes

[Justin Lemkul]

On 2/19/14, 1:05 PM, Jeff Chen wrote:

Dear All,

I am trying to calculate the change in free energy that occurs when
charging multiple type B molecules in an A-B mixture. For example, I have a
mixture of 900 molecules of type A and 100 of type B. When coulomb
interactions are on, B is identical to A (something like TIP4P water), but
when coulomb interactions are off, each B is simply a Lennard-Jones
particle (in the topology file, I've labelled B differently and called the
molecule SOLB, but all interaction information is identical to A). To do
the free energy calculations, I perform different simulations at each
lambda point. For example, for a simulation with lambda=0, I have the
following in my .mdp file:

free_energy = yes
init_lambda = 0.0
delta_lambda = 0
foreign_lambda= 0.05
couple-lambda0=vdw-q
couple-lambda1=vdw
couple-moltype=SOLB

and when lamba=1,

free_energy = yes
init_lambda = 1.0
delta_lambda = 0
foreign_lambda= 0.95
couple-lambda0=vdw-q
couple-lambda1=vdw
couple-moltype=SOLB

I expected that when lambda=0, B molecules would behave identically to A
molecules with the coulombic energy fully turned on (couple-lambda0=vdw-q),
and when lambda=1, B molecules would behave like LJ particles, with no
coulombic interactions, either with each other, or with A molecules.

However, when I look at the coulombic energy for B-B interactions (I used
tpbconv -o to make a new *.tpr for only B molecules, then used mdrun -rerun
with a trajectory containing only information about B molecules), I find
that both the short-range and reciprocal coulombic energies are NOT zero as
I had expected for lambda = 1, and are in fact exactly equal to the
negative of the respective coulombic energies obtained using the same
trajectory data when lambda=0.


What are the energies without using tpbconv and mdrun -rerun?  In other words, 
it's necessary to figure out whether this is a problem in the original 
simulation with the free energy code (unlikely, given how simple the system is) 
or a problem using mdrun -rerun in conjunction with the free energy code (far 
more likely).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Free energy calculation problems (bug?)

[asaffarhi]

Dear Prof. Shirts

We also have a few questions on that issue and we will really  
appreciate your help.


If we understand correctly:

 coupl-intramol = yes - remove all interactions of the decoupled atoms
 coupl-intramol = no - remove only solute solvent interactions pf the  
decoupled atoms.


You previuosly wrote:
" if one sets coupl-intramol = yes, LJ and Coul 1-4's
are left on (uncoupled) at all lambda. The actual bug is fixed in 5.0
(actually, in 4.6.4). "

The questions are the following:
1. Is there a way to remove also these 1-4's?
2. Is there a tutorial for relative free energy calculation so we can  
verify what we do?
3. Can we use charge at the end state B (rather than zero) ? is the  
same behavior expected with the coupl-intramol parameter when if we  
change the charge to a value other than zero?


4. Is this the proper way to turn charge off (through the topology file)?

 nr type resnr resid atom cgnr charge mass typeB chargeB  massB
 1   HC   1PCH3   H1   1   0.123 1.0080 HC 0.01.0080

5. What is the proper way to turn VDW off and could the VDW parameters  
also be changed to another value rather than zero?


Thanks in advance,
Best regards,
Asaf

Quoting Олег Титов :


What should I do to be able to file a redmine? I've registered at
redmine.gromacs.org, but the account is waiting for confirmation for 2
days. Should I do anything else, or it's ok?


2014-02-08 18:49 GMT+04:00 Michael Shirts :


Two thoughts that probably don't explain the problem, since they
should have similar behavior between versions:

* vdw-type = Cut-off

is almost never a good idea.  If you are doing this to be
reproducible, it's fine, but I'd avoid it in the future.

* You almost certainly want DispCorr = EnerPres, or else the density
will change with cutoff, and dispersion interactions beyond the cutoff
will be neglected (also changing the energy with cutoff).

Can you file a redmine (http://redmine.gromacs.org) with .top  and
.gro files as well?  One never knows where a problem might be coming
from (maybe only with certain top files?), so having those helps as
well.  It would be better to have the softcore version, since that is
likely to be better behaved anyway, and it has the same difference.


On Sat, Feb 8, 2014 at 12:00 AM, Олег Титов 
wrote:
> Dear GROMACS users!
>
> I've encountered a problem in thermodynamic integration with GROMACS. I'm
> interested in calculating of solvation free energy differences between
> holbenzenes and benzene. To calculate this values I use thermodynamic
> integration approach (5 point formula).
>
> Half a year ago I did my calculation with GROMACS 4.6.1. The results
looked
> good and were consistent with literature data. Recently, I've discovered
> that versions 4.6.0 and 4.6.1 had a bug in free energy code, so I decided
> to recalculate everything with 4.6.5 version of GROMACS. New results look
> not so good and, moreover, are not consistent with literature.
>
> I use GAFF forcefield with TIP3P water models. To obtain GROMACS topology
> and coordinate files I convert AMBER topologies (generated with tleap)
with
> amb2gmx.pl script and this topologies look fine.
>
>  For phenylbromide molecule calculated solvation free difference should
be
> near -0.1 - -0.2 kcal/mol (Experimental data is 0.59 kcal/mol).
> 4.6.1 version gave me -0.1+-0.13 kcal/mol - Fine!
> I've performed the same calculation with AMBER11  - -0.27 +-0.16
kcal/mol -
> also fine.
> 4.6.5 version for the same system gives me 1.1 - 1.2 kcal/mol
>
> I've played with some options (tried adding soft-core potentials and
turned
> on/off couple-intramol option). The results are:
> no_sc no_intramol 1.27 +- 0.18
> no_sc intramol 1.20 +- 0.20
> sc no_intramol 1.35 +- 0.21
> sc intramol 1.22 +- 0.19
>
> So now I don't know what to do. Old buggy version produced good results
> consistent with literature and other MD packages and new fixed version
> produces different results. The dH/dl curve for two versions of GROMACS
> looks similar for lambdas 0-0.7 (mutation is PhBr -> PhH ) but becomes
> different at lambda = 0.9 So something changed there... Moreover
different
> elecrostatic approaches for PhBr molecule are consistent with each other
> (dddG are fine), but new version of GROMACS gives me overestimated ddG as
> shown above.
>
> Can anyone give me some advice what to do with it? May be there is some
bug
> in new version? May be I'm doing something wrong?
>
> Attaching sample .mdp (for solvated and vacuum system) and .top files.
>
> Thanks for the help,
> Oleg
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
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htt

Re: [gmx-users] Free energy calculation problems (bug?)

[Олег Титов]

What should I do to be able to file a redmine? I've registered at
redmine.gromacs.org, but the account is waiting for confirmation for 2
days. Should I do anything else, or it's ok?


2014-02-08 18:49 GMT+04:00 Michael Shirts :

> Two thoughts that probably don't explain the problem, since they
> should have similar behavior between versions:
>
> * vdw-type = Cut-off
>
> is almost never a good idea.  If you are doing this to be
> reproducible, it's fine, but I'd avoid it in the future.
>
> * You almost certainly want DispCorr = EnerPres, or else the density
> will change with cutoff, and dispersion interactions beyond the cutoff
> will be neglected (also changing the energy with cutoff).
>
> Can you file a redmine (http://redmine.gromacs.org) with .top  and
> .gro files as well?  One never knows where a problem might be coming
> from (maybe only with certain top files?), so having those helps as
> well.  It would be better to have the softcore version, since that is
> likely to be better behaved anyway, and it has the same difference.
>
>
> On Sat, Feb 8, 2014 at 12:00 AM, Олег Титов 
> wrote:
> > Dear GROMACS users!
> >
> > I've encountered a problem in thermodynamic integration with GROMACS. I'm
> > interested in calculating of solvation free energy differences between
> > holbenzenes and benzene. To calculate this values I use thermodynamic
> > integration approach (5 point formula).
> >
> > Half a year ago I did my calculation with GROMACS 4.6.1. The results
> looked
> > good and were consistent with literature data. Recently, I've discovered
> > that versions 4.6.0 and 4.6.1 had a bug in free energy code, so I decided
> > to recalculate everything with 4.6.5 version of GROMACS. New results look
> > not so good and, moreover, are not consistent with literature.
> >
> > I use GAFF forcefield with TIP3P water models. To obtain GROMACS topology
> > and coordinate files I convert AMBER topologies (generated with tleap)
> with
> > amb2gmx.pl script and this topologies look fine.
> >
> >  For phenylbromide molecule calculated solvation free difference should
> be
> > near -0.1 - -0.2 kcal/mol (Experimental data is 0.59 kcal/mol).
> > 4.6.1 version gave me -0.1+-0.13 kcal/mol - Fine!
> > I've performed the same calculation with AMBER11  - -0.27 +-0.16
> kcal/mol -
> > also fine.
> > 4.6.5 version for the same system gives me 1.1 - 1.2 kcal/mol
> >
> > I've played with some options (tried adding soft-core potentials and
> turned
> > on/off couple-intramol option). The results are:
> > no_sc no_intramol 1.27 +- 0.18
> > no_sc intramol 1.20 +- 0.20
> > sc no_intramol 1.35 +- 0.21
> > sc intramol 1.22 +- 0.19
> >
> > So now I don't know what to do. Old buggy version produced good results
> > consistent with literature and other MD packages and new fixed version
> > produces different results. The dH/dl curve for two versions of GROMACS
> > looks similar for lambdas 0-0.7 (mutation is PhBr -> PhH ) but becomes
> > different at lambda = 0.9 So something changed there... Moreover
> different
> > elecrostatic approaches for PhBr molecule are consistent with each other
> > (dddG are fine), but new version of GROMACS gives me overestimated ddG as
> > shown above.
> >
> > Can anyone give me some advice what to do with it? May be there is some
> bug
> > in new version? May be I'm doing something wrong?
> >
> > Attaching sample .mdp (for solvated and vacuum system) and .top files.
> >
> > Thanks for the help,
> > Oleg
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Free energy calculation problems (bug?)

[Олег Титов]

Thank you for your reply, Dr Shirts.

I'll recalculate my energies with vdw-type = shift and DispCorr = EnerPres
and enabled softcore with both old and new version of GROMACS. However, I'm
not sure if softcore is necessary since aromatic hydrogens have VdW
potentials in GAFF so no atom disappears in this particular system.

If nothing changes, i'll file a readmine asap.


2014-02-08 18:49 GMT+04:00 Michael Shirts :

> Two thoughts that probably don't explain the problem, since they
> should have similar behavior between versions:
>
> * vdw-type = Cut-off
>
> is almost never a good idea.  If you are doing this to be
> reproducible, it's fine, but I'd avoid it in the future.
>
> * You almost certainly want DispCorr = EnerPres, or else the density
> will change with cutoff, and dispersion interactions beyond the cutoff
> will be neglected (also changing the energy with cutoff).
>
> Can you file a redmine (http://redmine.gromacs.org) with .top  and
> .gro files as well?  One never knows where a problem might be coming
> from (maybe only with certain top files?), so having those helps as
> well.  It would be better to have the softcore version, since that is
> likely to be better behaved anyway, and it has the same difference.
>
>
> On Sat, Feb 8, 2014 at 12:00 AM, Олег Титов 
> wrote:
> > Dear GROMACS users!
> >
> > I've encountered a problem in thermodynamic integration with GROMACS. I'm
> > interested in calculating of solvation free energy differences between
> > holbenzenes and benzene. To calculate this values I use thermodynamic
> > integration approach (5 point formula).
> >
> > Half a year ago I did my calculation with GROMACS 4.6.1. The results
> looked
> > good and were consistent with literature data. Recently, I've discovered
> > that versions 4.6.0 and 4.6.1 had a bug in free energy code, so I decided
> > to recalculate everything with 4.6.5 version of GROMACS. New results look
> > not so good and, moreover, are not consistent with literature.
> >
> > I use GAFF forcefield with TIP3P water models. To obtain GROMACS topology
> > and coordinate files I convert AMBER topologies (generated with tleap)
> with
> > amb2gmx.pl script and this topologies look fine.
> >
> >  For phenylbromide molecule calculated solvation free difference should
> be
> > near -0.1 - -0.2 kcal/mol (Experimental data is 0.59 kcal/mol).
> > 4.6.1 version gave me -0.1+-0.13 kcal/mol - Fine!
> > I've performed the same calculation with AMBER11  - -0.27 +-0.16
> kcal/mol -
> > also fine.
> > 4.6.5 version for the same system gives me 1.1 - 1.2 kcal/mol
> >
> > I've played with some options (tried adding soft-core potentials and
> turned
> > on/off couple-intramol option). The results are:
> > no_sc no_intramol 1.27 +- 0.18
> > no_sc intramol 1.20 +- 0.20
> > sc no_intramol 1.35 +- 0.21
> > sc intramol 1.22 +- 0.19
> >
> > So now I don't know what to do. Old buggy version produced good results
> > consistent with literature and other MD packages and new fixed version
> > produces different results. The dH/dl curve for two versions of GROMACS
> > looks similar for lambdas 0-0.7 (mutation is PhBr -> PhH ) but becomes
> > different at lambda = 0.9 So something changed there... Moreover
> different
> > elecrostatic approaches for PhBr molecule are consistent with each other
> > (dddG are fine), but new version of GROMACS gives me overestimated ddG as
> > shown above.
> >
> > Can anyone give me some advice what to do with it? May be there is some
> bug
> > in new version? May be I'm doing something wrong?
> >
> > Attaching sample .mdp (for solvated and vacuum system) and .top files.
> >
> > Thanks for the help,
> > Oleg
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Free energy calculation problems (bug?)

[Michael Shirts]

Two thoughts that probably don't explain the problem, since they
should have similar behavior between versions:

* vdw-type = Cut-off

is almost never a good idea.  If you are doing this to be
reproducible, it's fine, but I'd avoid it in the future.

* You almost certainly want DispCorr = EnerPres, or else the density
will change with cutoff, and dispersion interactions beyond the cutoff
will be neglected (also changing the energy with cutoff).

Can you file a redmine (http://redmine.gromacs.org) with .top  and
.gro files as well?  One never knows where a problem might be coming
from (maybe only with certain top files?), so having those helps as
well.  It would be better to have the softcore version, since that is
likely to be better behaved anyway, and it has the same difference.


On Sat, Feb 8, 2014 at 12:00 AM, Олег Титов  wrote:
> Dear GROMACS users!
>
> I've encountered a problem in thermodynamic integration with GROMACS. I'm
> interested in calculating of solvation free energy differences between
> holbenzenes and benzene. To calculate this values I use thermodynamic
> integration approach (5 point formula).
>
> Half a year ago I did my calculation with GROMACS 4.6.1. The results looked
> good and were consistent with literature data. Recently, I've discovered
> that versions 4.6.0 and 4.6.1 had a bug in free energy code, so I decided
> to recalculate everything with 4.6.5 version of GROMACS. New results look
> not so good and, moreover, are not consistent with literature.
>
> I use GAFF forcefield with TIP3P water models. To obtain GROMACS topology
> and coordinate files I convert AMBER topologies (generated with tleap) with
> amb2gmx.pl script and this topologies look fine.
>
>  For phenylbromide molecule calculated solvation free difference should be
> near -0.1 - -0.2 kcal/mol (Experimental data is 0.59 kcal/mol).
> 4.6.1 version gave me -0.1+-0.13 kcal/mol - Fine!
> I've performed the same calculation with AMBER11  - -0.27 +-0.16 kcal/mol -
> also fine.
> 4.6.5 version for the same system gives me 1.1 - 1.2 kcal/mol
>
> I've played with some options (tried adding soft-core potentials and turned
> on/off couple-intramol option). The results are:
> no_sc no_intramol 1.27 +- 0.18
> no_sc intramol 1.20 +- 0.20
> sc no_intramol 1.35 +- 0.21
> sc intramol 1.22 +- 0.19
>
> So now I don't know what to do. Old buggy version produced good results
> consistent with literature and other MD packages and new fixed version
> produces different results. The dH/dl curve for two versions of GROMACS
> looks similar for lambdas 0-0.7 (mutation is PhBr -> PhH ) but becomes
> different at lambda = 0.9 So something changed there... Moreover different
> elecrostatic approaches for PhBr molecule are consistent with each other
> (dddG are fine), but new version of GROMACS gives me overestimated ddG as
> shown above.
>
> Can anyone give me some advice what to do with it? May be there is some bug
> in new version? May be I'm doing something wrong?
>
> Attaching sample .mdp (for solvated and vacuum system) and .top files.
>
> Thanks for the help,
> Oleg
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
>
-- 
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* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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