[gmx-users] symmetrical LJ binary mixture simulation

[Hyuntae Jung]

Hello, gromacs users.


I wonder if it is possible to simulate a symmetrical LJ binary mixture 
implementing LJ-PME methods.


The mixture is composed of A and B-type LJ particles and their sizes (sigma) 
are unity (=1). The interaction energy (epsilon) of A-A and B-B is unity, but 
heterogeneous interaction (A-B) is 0.5. While I try to apply LJ-PME method, the 
parameter, "lj-pme-comb-rule" is not supported for this case (Either geometric 
or LB combination rule is allowed).


Is there any possible way to work such an user-defined combination rule using 
LJ-PME method in Gromacs?  If not possible in Gromacs, any simulation packages 
which supports those system with LJ-PME?


Sincerely,

Hyuntae Jung

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Re: [gmx-users] Perturbation Thermodynamic Integration

[Hannes Loeffler]

On Tue, 16 May 2017 15:13:10 -0400
Dan Gil  wrote:


> If you do this via decoupling ("absolute" transformation) you do that
> > once for molecule A and once for molecule B.  
> 
> 
> I believe you are referring to the BAR method? I am trying to see if
> I get the same results as another group. They used thermodynamic
> integration from A to B, so I decided to spend some more time with
> this. I will try later if I get consistent results for both methods.

No, I am not referring to a specific analysis methods.  I commented on
an alternative pathway.


> transforming the masses may interact badly
> > with bond constraints that are applied to alchemically transformed
> > bonds  
> 
> 
> Thank you for this information! Do you know if there are there
> publications that refer to this issue?

Not that I know of.
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Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

>
> What does grompp from 2016.3 report?
>

ERROR 1 [file topol.top, line 10]:
  Atom 1 in molecule type 'HEPT' has different A and B state charges and/or
  atom types set in the topology file as well as through the mdp option
  'couple-moltype'. You can not use both these methods simultaneously.

If you do this via decoupling ("absolute" transformation) you do that
> once for molecule A and once for molecule B.


I believe you are referring to the BAR method? I am trying to see if I get
the same results as another group. They used thermodynamic integration from
A to B, so I decided to spend some more time with this. I will try later if
I get consistent results for both methods.

If you want to do this via a relative transformation you would not use
> couple-moltype at all but fill in the B columns in your topology file
> for all force field parameters that change.


I've filled in the B columns, but I didn't realize that I should not use
couple-moltype. I will remove the following lines from mdp file.

couple-moltype   = HEPT
> couple-lambda0   = vdwq
> couple-lambda1   = none
> couple-intramol  = no


Then, grompp reports no errors.

transforming the masses may interact badly
> with bond constraints that are applied to alchemically transformed
> bonds


Thank you for this information! Do you know if there are there publications
that refer to this issue?

On Tue, May 16, 2017 at 10:46 AM, Hannes Loeffler <
hannes.loeff...@stfc.ac.uk> wrote:

> On Tue, 16 May 2017 10:28:08 -0400
> Dan Gil  wrote:
>
> > Thank you for the advice on the cut-off schemes and PME methods.
> >
> > What is the physical meaning of a non-interacting final state
> > > that has different masses from the initial state?
> >
> >
> > These free energy options was just from me trying to figure out why
> > mass has any contributions at all. I am going from molecule A to B
> > described in the topology. In the actual simulations, I am planning
> > on using this: vdw_lambdas  = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 coul_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 bonded_lambdas   = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 restraint_lambdas= 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1
> >
> > To get the solvation free energy difference between molecule A and B.
>
> If you do this via decoupling ("absolute" transformation) you do that
> once for molecule A and once for molecule B.  I don't see why you would
> want to change masses in this case.
>
> If you want to do this via a relative transformation you would not use
> couple-moltype at all but fill in the B columns in your topology file
> for all force field parameters that change.  In this case you _can_
> change the masses but you would have to do the same transformation in
> vacuum. Then the mass contributions should cancel perfectly (at least in
> the limit of infinite sampling, I guess).  But Michael Shirts has
> commented a while back that transforming the masses may interact badly
> with bond constraints that are applied to alchemically transformed
> bonds (we have seen problems with this too). So it is just simplest to
> not use mass-lambdas precisely because of the aforementioned argument.
>
>
> Cheers,
> Hannes.
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Re: [gmx-users] Protein-Ligand

[Justin Lemkul]

On 5/16/17 1:31 PM, RAHUL SURESH wrote:

Dear Justin
Thank you much.

About the term "curved", even am not exactly clear about it. Book by prof
Pamela states that sentence. As I feel she must be explaining about much
deformed protein.



Well, that's too many unknowns.  If you're worried about a problem that you 
don't understand, there's little I can suggest as a solution.  There are 
proteins that bend, e.g. to remodel membranes or form higher-order structures 
but that seems to be entirely irrelevant to a case of protein-ligand 
dissociation.  Be very sure that it's not a simple PBC issue, and as I suggested 
before, watch the trajectory to see the details of what's happening.


-Justin



On Tue, 16 May 2017 at 7:41 PM, Justin Lemkul  wrote:




On 5/15/17 9:12 AM, RAHUL SURESH wrote:

Dear Users

I am tryjng to simulate protein ligand complex using charmm36ff for

100ns.

I found the ligand moving away from the protein around 55ns. I don't

think

it s a pbc effect. Is there anything I have done wrong or Should I add

any

additional commands.?
Await your valuable advice.



Watch the trajectory and see which interactions break first.  Then
consider if
your ligand topology needs refinement to deal with such interactions or if
it's
trying to sample some strained conformation that is incompatible with
binding
(suggesting an internal/dihedral problem).  Compare with available
experimental
data; some things just have weak affinity.


PS: Will the ligand move out of protein if the protein is over curved

after

interaction?



What does "over curved" mean?

-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] Problems with large molecule simulation

[Justin Lemkul]

On 5/16/17 1:32 PM, Tam, Benjamin wrote:

Hi Justin,

Thank you for replying, the problem is this:

Fatal error:
Atomtype Zr110418 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

because the number and the name combine together i.e. supposed to be Zr1 10418. 
How can I solve this problem?



That error is coming from the topology, not the coordinate file.

-Justin


Best regards,

Ben

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 16 May 2017 18:30
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problems with large molecule simulation



On 5/16/17 1:27 PM, Ben Tam wrote:


Dear gromacs user,

I am trying to simulate a large system, but I ran into some fundamental 
problems. For example in the .gro file, the name of the atoms merge with the 
number count:

2MOL C2 9998   3.987   2.259   6.276
2MOL C5    3.987   2.061   6.079
2MOL C11   3.987   1.025   7.721
2MOL C210001   3.987   0.920   7.615

Sorry for this basic question, but how do people solve that problem? As I know 
there is a specific format for .gro file?



Yes, it is fixed-format.

http://manual.gromacs.org/documentation/2016.3/user-guide/file-formats.html#gro

What exactly is the nature of the problem?  Most common systems are >10k atoms 
and all GROMACS tools should handle things just fine.

-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] Problems with large molecule simulation

[Tam, Benjamin]

Hi Justin,

Thank you for replying, the problem is this:

Fatal error:
Atomtype Zr110418 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

because the number and the name combine together i.e. supposed to be Zr1 10418. 
How can I solve this problem?

Best regards,

Ben

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 16 May 2017 18:30
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problems with large molecule simulation



On 5/16/17 1:27 PM, Ben Tam wrote:
>
> Dear gromacs user,
>
> I am trying to simulate a large system, but I ran into some fundamental 
> problems. For example in the .gro file, the name of the atoms merge with the 
> number count:
>
> 2MOL C2 9998   3.987   2.259   6.276
> 2MOL C5    3.987   2.061   6.079
> 2MOL C11   3.987   1.025   7.721
> 2MOL C210001   3.987   0.920   7.615
>
> Sorry for this basic question, but how do people solve that problem? As I 
> know there is a specific format for .gro file?
>

Yes, it is fixed-format.

http://manual.gromacs.org/documentation/2016.3/user-guide/file-formats.html#gro

What exactly is the nature of the problem?  Most common systems are >10k atoms 
and all GROMACS tools should handle things just fine.

-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] Protein-Ligand

[RAHUL SURESH]

Dear Justin
Thank you much.

About the term "curved", even am not exactly clear about it. Book by prof
Pamela states that sentence. As I feel she must be explaining about much
deformed protein.


On Tue, 16 May 2017 at 7:41 PM, Justin Lemkul  wrote:

>
>
> On 5/15/17 9:12 AM, RAHUL SURESH wrote:
> > Dear Users
> >
> > I am tryjng to simulate protein ligand complex using charmm36ff for
> 100ns.
> > I found the ligand moving away from the protein around 55ns. I don't
> think
> > it s a pbc effect. Is there anything I have done wrong or Should I add
> any
> > additional commands.?
> > Await your valuable advice.
> >
>
> Watch the trajectory and see which interactions break first.  Then
> consider if
> your ligand topology needs refinement to deal with such interactions or if
> it's
> trying to sample some strained conformation that is incompatible with
> binding
> (suggesting an internal/dihedral problem).  Compare with available
> experimental
> data; some things just have weak affinity.
>
> > PS: Will the ligand move out of protein if the protein is over curved
> after
> > interaction?
> >
>
> What does "over curved" mean?
>
> -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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> * Please search the archive at
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> posting!
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>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Problems with large molecule simulation

[Tam, Benjamin]

Dear gromacs user,

I am trying to simulate a large system, but I ran into some fundamental 
problems. For example in the .gro file, the name of the atoms merge with the 
number count:

2MOL C2 9998   3.987   2.259   6.276
2MOL C5    3.987   2.061   6.079
2MOL C11   3.987   1.025   7.721
2MOL C210001   3.987   0.920   7.615

Sorry for this basic question, but how do people solve that problem? As I know 
there is a specific format for .gro file?

Thank you very much for your help.

Best regards,

Benjamin Tam

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Re: [gmx-users] Problems with large molecule simulation

[Justin Lemkul]

On 5/16/17 1:27 PM, Ben Tam wrote:


Dear gromacs user,

I am trying to simulate a large system, but I ran into some fundamental 
problems. For example in the .gro file, the name of the atoms merge with the 
number count:

2MOL C2 9998   3.987   2.259   6.276
2MOL C5    3.987   2.061   6.079
2MOL C11   3.987   1.025   7.721
2MOL C210001   3.987   0.920   7.615

Sorry for this basic question, but how do people solve that problem? As I know 
there is a specific format for .gro file?



Yes, it is fixed-format.

http://manual.gromacs.org/documentation/2016.3/user-guide/file-formats.html#gro

What exactly is the nature of the problem?  Most common systems are >10k atoms 
and all GROMACS tools should handle things just fine.


-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] Problems with large molecule simulation

[Ben Tam]

Dear gromacs user,

I am trying to simulate a large system, but I ran into some fundamental 
problems. For example in the .gro file, the name of the atoms merge with the 
number count:

2MOL C2 9998   3.987   2.259   6.276
2MOL C5    3.987   2.061   6.079
2MOL C11   3.987   1.025   7.721
2MOL C210001   3.987   0.920   7.615

Sorry for this basic question, but how do people solve that problem? As I know 
there is a specific format for .gro file?

Thank you very much for your help.

Best regards,

Benjamin Tam

-- 
Gromacs Users mailing list

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Re: [gmx-users] Fwd: Issue with parallel simulations in vacuum

[Agusti Emperador]

Thanks very much Mark

In fact, the results that I find are pathological in the sense that the
kinetic energy does not seem to be correctly distributed along the system:
one of the proteins seems to be at much lower temperature than the other
one (according to their conformational sampling; they are disordered
proteins)

Best regards

Agusti



On Tue, May 16, 2017 at 4:19 PM, Mark Abraham 
wrote:

> Hi,
>
> In GROMACS 4.6.6 we added a fatal error for Andersen+constraints+domain
> decomposition with more than one domain, because it gave a temperature that
> is obviously too high. So, I presume Michael Shirts never implemented it to
> work / tested it with particle decomposition, either.
>
> Fortunately, 600 particles isn't likely to show an appreciable speedup for
> more than one rank, so I'd stay on a single rank, or update to a recent
> GROMACS and use Verlet + md + v-rescale.
>
> Mark
>
> On Tue, May 16, 2017 at 4:05 PM Justin Lemkul  wrote:
>
> >
> >
> > On 5/16/17 7:26 AM, Agusti Emperador wrote:
> > > Dear GROMACS experts,
> > >
> > > I am simulating a system of two disordered proteins in vacuum. I use
> > > gromacs 4.6.5. The serial simulation works fine, but when I run it in
> > > parallel (2 processors) it gives seriously pathological results.
> > >
> > > I use particle decomposition and periodic boundary conditions, because
> I
> > > want to simulate a solution at a certain concentration (technically,
> the
> > > simulation is in vacuum, but I have included the effects of solvation
> in
> > > the nonbonded terms of the force field in my coarse-grained protein
> > model).
> > > Each protein has 300 particles.
> > >
> > > I use exactly the same parameters and input files in the serial
> > simulation
> > > and in the parallel simulation. This is the mdp file that I use:
> > >
> > > integrator   =  md-vv
> > > dt   =  0.02
> > > nsteps   =  5
> > > nstxout  =  0
> > > nstvout  =  0
> > > nstenergy = 50
> > > nstlog   =  50
> > > nstxtcout=  5
> > > nstcomm = 1
> > > nstcalcenergy = 1
> > > xtc-precision=  10
> > > rlist=  1.4
> > > coulombtype  =  shift
> > > rcoulomb =  1.2
> > > epsilon_r=  15
> > > vdw-type =  shift
> > > rvdw-switch  =  0.9
> > > rvdw =  1.2
> > > tcoupl   =  andersen
> > > tc-grps  =  Protein
> > > tau-t=  .1
> > > ref-t=  300
> > > Pcoupl   =  no
> > > refcoord_scaling =  all
> > >
> > > It works perfectly in the serial simulation, but I need to make
> parallel
> > > simulations in order to simulate systems with many proteins.
> > >
> > > How could I solve the problem?
> > >
> >
> > What is the problem?  What do you define as "seriously pathological
> > results" in
> > this case?  Also note that 4.6.5 is practically prehistoric and you may
> > wish to
> > consider a newer, faster, less-buggy version of the code.
> >
> > -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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Re: [gmx-users] Perturbation Thermodynamic Integration

[Hannes Loeffler]

On Tue, 16 May 2017 10:28:08 -0400
Dan Gil  wrote:

> Thank you for the advice on the cut-off schemes and PME methods.
> 
> What is the physical meaning of a non-interacting final state
> > that has different masses from the initial state?  
> 
> 
> These free energy options was just from me trying to figure out why
> mass has any contributions at all. I am going from molecule A to B
> described in the topology. In the actual simulations, I am planning
> on using this: vdw_lambdas  = 0 0.1 0.2 0.3 0.4 0.5 0.6
> 0.7 0.8 0.9 1 coul_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6
> 0.7 0.8 0.9 1 bonded_lambdas   = 0 0.1 0.2 0.3 0.4 0.5 0.6
> 0.7 0.8 0.9 1 restraint_lambdas= 0 0.1 0.2 0.3 0.4 0.5 0.6
> 0.7 0.8 0.9 1 mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6
> 0.7 0.8 0.9 1
> 
> To get the solvation free energy difference between molecule A and B.

If you do this via decoupling ("absolute" transformation) you do that
once for molecule A and once for molecule B.  I don't see why you would
want to change masses in this case.

If you want to do this via a relative transformation you would not use
couple-moltype at all but fill in the B columns in your topology file
for all force field parameters that change.  In this case you _can_
change the masses but you would have to do the same transformation in
vacuum. Then the mass contributions should cancel perfectly (at least in
the limit of infinite sampling, I guess).  But Michael Shirts has
commented a while back that transforming the masses may interact badly
with bond constraints that are applied to alchemically transformed
bonds (we have seen problems with this too). So it is just simplest to
not use mass-lambdas precisely because of the aforementioned argument.


Cheers,
Hannes.
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[gmx-users] Hydroxyl bonds rotating too much

[Juan José Galano Frutos]

Thank you Justin. The problematic OH is part of the cofactor molecule.
This OH group is located in an extreme part of the cofactor so it
apparently only interacts with solvent, not with the protein.

I'm doing just now some tests of the cofactor solvated in order to
check if the problem comes from the cofactor itself or comes from
other issue.

I'll post here the result of this test whatever it is.

Thank you again.

Best


On 5/16/17 7:03 AM, Juan José Galano Frutos wrote:
>* Hi there:
*>>* I am simulating a protein which include as a cofactor a molecule bearing
*>* some hydroxyl groups. The system is crashing from the begining of the
*>* equilibration step (after the following steps: vaccuum minimization,
*>* solvating, neutralizing, minimization, heating) due to -in all the
*>* replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
*>* degrees.
*>* I checked the structures and the systems looking for either water or
*>* protein parts in so close contact with this hydroxyl groups, but it was not
*>* the case. Then I proceeded to re-minimize again the systems after the
*>* heating step and afterward to relaunch the equilibration step, but again
*>* the same happened. I also checked the topology file of this cofactor but
*>* all seems to be fine, I mean charges.
*>* Then, what could be happening? Is it common this behaviour in hydroxyl
*>* groups?Any help please
*>
What does the problematic OH group interact with?  The over-rotation is a
symptom, not a cause.  If it interacts with your cofactor, the parameters for
that cofactor are likely suspect.  Typical diagnostic steps are in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

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

==




Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Thank you for the advice on the cut-off schemes and PME methods.

What is the physical meaning of a non-interacting final state
> that has different masses from the initial state?


These free energy options was just from me trying to figure out why mass
has any contributions at all. I am going from molecule A to B described in
the topology. In the actual simulations, I am planning on using this:
vdw_lambdas  = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
coul_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
bonded_lambdas   = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
restraint_lambdas= 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

To get the solvation free energy difference between molecule A and B.

You'd need the latest grompp, as I've mentioned twice.


Sorry, I wasn't sure if I had the right version of grompp or not. I am
seeing if I can download the newest version of Gromacs to check.

On Tue, May 16, 2017 at 10:10 AM, Hannes Loeffler <
hannes.loeff...@stfc.ac.uk> wrote:

> I have not really followed the previous email exchange but from this
> mdp file I wonder what you are trying to achieve.  You seem to want to
> decouple all atoms of your HEPT molecule (couple-moltype,
> couple-intramol) from its environment but then you also change the
> masses.  What is the physical meaning of a non-interacting final state
> that has different masses from the initial state?  I believe the mass
> contributions are supposed to cancel in a closed thermodynamic cycle
> but what is the cycle you are simulating?
>
>
> On Tue, 16 May 2017 09:30:08 -0400
> Dan Gil  wrote:
>
> > Sorry, here is the mdp file:
> >
> > ;Integration Method and Parameters
> > integrator   = sd
> > nsteps   = 10
> > dt = 0.002
> > nstenergy= 1000
> > nstlog   = 5000
> >
> > ;Output Control
> > nstxout = 0
> > nstvout = 0
> >
> > ;Cutoff Schemes
> > cutoff-scheme= group
> > rlist= 1.0
> > vdw-type = cut-off
> > rvdw = 2.0
> >
> > ;Coulomb interactions
> > coulombtype  = pme
> > rcoulomb = 1.0
> > fourierspacing   = 0.4
> >
> > ;Constraints
> > constraints  = all-bonds
> >
> > ;Temperature coupling
> > tcoupl   = v-rescale
> > tc-grps  = system
> > tau-t= 0.1
> > ref-t= 300
> >
> > ;Pressure coupling
> > pcoupl = parrinello-rahman
> > ref-p = 1.01325
> > compressibility = 4.5e-5
> > tau-p = 5
> >
> > ;Free energy calculation
> > free-energy  = yes
> > init-lambda-state= 8
> > delta-lambda = 0
> > fep-lambdas  =
> > calc-lambda-neighbors= 1
> > vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
> > coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
> > bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
> > restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
> > mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> > couple-moltype   = HEPT
> > couple-lambda0   = vdwq
> > couple-lambda1   = none
> > couple-intramol  = no
> > nstdhdl  = 10
> >
> >
> > On Tue, May 16, 2017 at 1:02 AM, Mark Abraham
> >  wrote:
> >
> > > Hi,
> > >
> > > What use are you making of constraints? Justin suggested sharing a
> > > full mdp file, which I think may help. We discovered last year that
> > > you can get equipartition failure for (IIRC) all-bonds constraints
> > > for moieties like -CH2Cl, and latest grompp now detects this.
> > >
> > > Mark
> > >
> > > On Tue, 16 May 2017 01:16 Dan Gil  wrote:
> > >
> > > > Hello,
> > > >
> > > > The last thread was getting too big, and the conversation evolved
> > > > to a topic different from my original question, so I decided to
> > > > start a new thread.
> > > >
> > > > We were discussing thermodynamic integration, and why the
> > > > mass_lambdas would have any contribution to the derivative of the
> > > > Hamiltonian.
> > > >
> > > > I found a source (link below) which derives the Gibbs free energy
> > > > change
> > > as
> > > > a function of lambda. I learned that the mass contribution is
> > > > often
> > > assumed
> > > > to be small and negligible, given that the mass difference
> > > > between the
> > > two
> > > > lambda states are small.
> > > > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> > > >
> > > > I think that the mass of the two lambda states that equation (14)
> > > > is referring to is the total mass (mass of solvent plus solute).
> > > > My system
> > > is
> > > > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I
> > > > wonder if I am getting nonzero mass contributions (in my dhdl.xvg
> > > > output) because of finite-size effects? Would completely
> > > > neglec

Re: [gmx-users] Fwd: Issue with parallel simulations in vacuum

[Mark Abraham]

Hi,

In GROMACS 4.6.6 we added a fatal error for Andersen+constraints+domain
decomposition with more than one domain, because it gave a temperature that
is obviously too high. So, I presume Michael Shirts never implemented it to
work / tested it with particle decomposition, either.

Fortunately, 600 particles isn't likely to show an appreciable speedup for
more than one rank, so I'd stay on a single rank, or update to a recent
GROMACS and use Verlet + md + v-rescale.

Mark

On Tue, May 16, 2017 at 4:05 PM Justin Lemkul  wrote:

>
>
> On 5/16/17 7:26 AM, Agusti Emperador wrote:
> > Dear GROMACS experts,
> >
> > I am simulating a system of two disordered proteins in vacuum. I use
> > gromacs 4.6.5. The serial simulation works fine, but when I run it in
> > parallel (2 processors) it gives seriously pathological results.
> >
> > I use particle decomposition and periodic boundary conditions, because I
> > want to simulate a solution at a certain concentration (technically, the
> > simulation is in vacuum, but I have included the effects of solvation in
> > the nonbonded terms of the force field in my coarse-grained protein
> model).
> > Each protein has 300 particles.
> >
> > I use exactly the same parameters and input files in the serial
> simulation
> > and in the parallel simulation. This is the mdp file that I use:
> >
> > integrator   =  md-vv
> > dt   =  0.02
> > nsteps   =  5
> > nstxout  =  0
> > nstvout  =  0
> > nstenergy = 50
> > nstlog   =  50
> > nstxtcout=  5
> > nstcomm = 1
> > nstcalcenergy = 1
> > xtc-precision=  10
> > rlist=  1.4
> > coulombtype  =  shift
> > rcoulomb =  1.2
> > epsilon_r=  15
> > vdw-type =  shift
> > rvdw-switch  =  0.9
> > rvdw =  1.2
> > tcoupl   =  andersen
> > tc-grps  =  Protein
> > tau-t=  .1
> > ref-t=  300
> > Pcoupl   =  no
> > refcoord_scaling =  all
> >
> > It works perfectly in the serial simulation, but I need to make parallel
> > simulations in order to simulate systems with many proteins.
> >
> > How could I solve the problem?
> >
>
> What is the problem?  What do you define as "seriously pathological
> results" in
> this case?  Also note that 4.6.5 is practically prehistoric and you may
> wish to
> consider a newer, faster, less-buggy version of the code.
>
> -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] Perturbation Thermodynamic Integration

[Hannes Loeffler]

I have not really followed the previous email exchange but from this
mdp file I wonder what you are trying to achieve.  You seem to want to
decouple all atoms of your HEPT molecule (couple-moltype,
couple-intramol) from its environment but then you also change the
masses.  What is the physical meaning of a non-interacting final state
that has different masses from the initial state?  I believe the mass
contributions are supposed to cancel in a closed thermodynamic cycle
but what is the cycle you are simulating?


On Tue, 16 May 2017 09:30:08 -0400
Dan Gil  wrote:

> Sorry, here is the mdp file:
> 
> ;Integration Method and Parameters
> integrator   = sd
> nsteps   = 10
> dt = 0.002
> nstenergy= 1000
> nstlog   = 5000
> 
> ;Output Control
> nstxout = 0
> nstvout = 0
> 
> ;Cutoff Schemes
> cutoff-scheme= group
> rlist= 1.0
> vdw-type = cut-off
> rvdw = 2.0
> 
> ;Coulomb interactions
> coulombtype  = pme
> rcoulomb = 1.0
> fourierspacing   = 0.4
> 
> ;Constraints
> constraints  = all-bonds
> 
> ;Temperature coupling
> tcoupl   = v-rescale
> tc-grps  = system
> tau-t= 0.1
> ref-t= 300
> 
> ;Pressure coupling
> pcoupl = parrinello-rahman
> ref-p = 1.01325
> compressibility = 4.5e-5
> tau-p = 5
> 
> ;Free energy calculation
> free-energy  = yes
> init-lambda-state= 8
> delta-lambda = 0
> fep-lambdas  =
> calc-lambda-neighbors= 1
> vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
> coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
> bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
> restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
> mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> couple-moltype   = HEPT
> couple-lambda0   = vdwq
> couple-lambda1   = none
> couple-intramol  = no
> nstdhdl  = 10
> 
> 
> On Tue, May 16, 2017 at 1:02 AM, Mark Abraham
>  wrote:
> 
> > Hi,
> >
> > What use are you making of constraints? Justin suggested sharing a
> > full mdp file, which I think may help. We discovered last year that
> > you can get equipartition failure for (IIRC) all-bonds constraints
> > for moieties like -CH2Cl, and latest grompp now detects this.
> >
> > Mark
> >
> > On Tue, 16 May 2017 01:16 Dan Gil  wrote:
> >  
> > > Hello,
> > >
> > > The last thread was getting too big, and the conversation evolved
> > > to a topic different from my original question, so I decided to
> > > start a new thread.
> > >
> > > We were discussing thermodynamic integration, and why the
> > > mass_lambdas would have any contribution to the derivative of the
> > > Hamiltonian.
> > >
> > > I found a source (link below) which derives the Gibbs free energy
> > > change  
> > as  
> > > a function of lambda. I learned that the mass contribution is
> > > often  
> > assumed  
> > > to be small and negligible, given that the mass difference
> > > between the  
> > two  
> > > lambda states are small.
> > > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> > >
> > > I think that the mass of the two lambda states that equation (14)
> > > is referring to is the total mass (mass of solvent plus solute).
> > > My system  
> > is  
> > > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I
> > > wonder if I am getting nonzero mass contributions (in my dhdl.xvg
> > > output) because of finite-size effects? Would completely
> > > neglecting the mass contributions  
> > be  
> > > acceptable? Does doing this technically change the system to one
> > > that is  
> > 1  
> > > solute and an infinite number of solvent molecules where the mass
> > > contributions limit is zero?
> > >
> > > Best Regards,
> > >
> > > Dan
> > > --
> > > 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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> > > or send a mail to gmx-users-requ...@gromacs.org.
> > >  
> > --
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> > or send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Perturbation Thermodynamic Integration

[Mark Abraham]

On Tue, May 16, 2017 at 3:54 PM Dan Gil  wrote:

> Hi,
>
> The latest version of Gromacs I have is 5.1. Using this version, grompp
> produces no warnings or errors.
>

I know you won't get the new warning from the old code ;-) You'd need the
latest grompp, as I've mentioned twice. If so, then that's a problem that
suggests a smaller time step. (But probably you have bigger problems.)


> I am using OPLS-AA, and I didn't have any issues with it thus far. I
> inherited this research project though 3 years ago. Is there something you
> think I should look at with scrutiny?
>

"No known issues" is not tantamount to "reliable model physics." If schemes
like that have been published and found useful, that's great. Otherwise,
you ought to have the burden of showing that it is a good model physics, or
throwing away the old work and doing something conventional (and if so, use
the verlet scheme and get much better performance).

Mark


> On Tue, May 16, 2017 at 9:42 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Yes that looks like it is the envelope of the new warning. What does
> grompp
> > from 2016.3 report?
> >
> > (Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd
> > reject that method immediately unless there was evidence that it worked
> > well for a range of observables, and was consistent with other practice
> for
> > that force field. If there is such evidence, for my information, what
> model
> > / force field does it like that?)
> >
> > Mark
> >
> > On Tue, May 16, 2017 at 3:30 PM Dan Gil  wrote:
> >
> > > Sorry, here is the mdp file:
> > >
> > > ;Integration Method and Parameters
> > > integrator   = sd
> > > nsteps   = 10
> > > dt = 0.002
> > > nstenergy= 1000
> > > nstlog   = 5000
> > >
> > > ;Output Control
> > > nstxout = 0
> > > nstvout = 0
> > >
> > > ;Cutoff Schemes
> > > cutoff-scheme= group
> > > rlist= 1.0
> > > vdw-type = cut-off
> > > rvdw = 2.0
> > >
> > > ;Coulomb interactions
> > > coulombtype  = pme
> > > rcoulomb = 1.0
> > > fourierspacing   = 0.4
> > >
> > > ;Constraints
> > > constraints  = all-bonds
> > >
> > > ;Temperature coupling
> > > tcoupl   = v-rescale
> > > tc-grps  = system
> > > tau-t= 0.1
> > > ref-t= 300
> > >
> > > ;Pressure coupling
> > > pcoupl = parrinello-rahman
> > > ref-p = 1.01325
> > > compressibility = 4.5e-5
> > > tau-p = 5
> > >
> > > ;Free energy calculation
> > > free-energy  = yes
> > > init-lambda-state= 8
> > > delta-lambda = 0
> > > fep-lambdas  =
> > > calc-lambda-neighbors= 1
> > > vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
> > > coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
> > > bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
> > > restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
> > > mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> > > couple-moltype   = HEPT
> > > couple-lambda0   = vdwq
> > > couple-lambda1   = none
> > > couple-intramol  = no
> > > nstdhdl  = 10
> > >
> > >
> > > On Tue, May 16, 2017 at 1:02 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > What use are you making of constraints? Justin suggested sharing a
> full
> > > mdp
> > > > file, which I think may help. We discovered last year that you can
> get
> > > > equipartition failure for (IIRC) all-bonds constraints for moieties
> > like
> > > > -CH2Cl, and latest grompp now detects this.
> > > >
> > > > Mark
> > > >
> > > > On Tue, 16 May 2017 01:16 Dan Gil  wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > The last thread was getting too big, and the conversation evolved
> to
> > a
> > > > > topic different from my original question, so I decided to start a
> > new
> > > > > thread.
> > > > >
> > > > > We were discussing thermodynamic integration, and why the
> > mass_lambdas
> > > > > would have any contribution to the derivative of the Hamiltonian.
> > > > >
> > > > > I found a source (link below) which derives the Gibbs free energy
> > > change
> > > > as
> > > > > a function of lambda. I learned that the mass contribution is often
> > > > assumed
> > > > > to be small and negligible, given that the mass difference between
> > the
> > > > two
> > > > > lambda states are small.
> > > > > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> > > > >
> > > > > I think that the mass of the two lambda states that equation (14)
> is
> > > > > referring to is the total mass (mass of solvent plus solute). My
> > system
> > > > is
> > > > > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I
> wonder
> > > if I
> > > > > am getting nonzero mass contributions

Re: [gmx-users] Protein-Ligand

[Justin Lemkul]

On 5/15/17 9:12 AM, RAHUL SURESH wrote:

Dear Users

I am tryjng to simulate protein ligand complex using charmm36ff for 100ns.
I found the ligand moving away from the protein around 55ns. I don't think
it s a pbc effect. Is there anything I have done wrong or Should I add any
additional commands.?
Await your valuable advice.



Watch the trajectory and see which interactions break first.  Then consider if 
your ligand topology needs refinement to deal with such interactions or if it's 
trying to sample some strained conformation that is incompatible with binding 
(suggesting an internal/dihedral problem).  Compare with available experimental 
data; some things just have weak affinity.



PS: Will the ligand move out of protein if the protein is over curved after
interaction?



What does "over curved" mean?

-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] 1-4 interactions in CHARMM force field

[Justin Lemkul]

On 5/15/17 2:02 PM, Dawid das wrote:

Dear Gromacs Users,

I would like to hear your advice on scaling 1,4-interactions for both
classical and
QM/MM molecular dynamics simulations. I am using CHARMM27 force field.

Firstly,  for classical MD, according to this post
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=1048

I should not rescale 1,4 iternactions, so if I use MDP options you suggest
on
Gromacs website I do not rescale them, right?



Right.  If you mess with 1-4 scaling, you invalidate the force field.  The 
dihedrals are parametrized under the assumption that 1-4 interactions are at 
full strength.  Dihedrals are correction factors for inaccuracies in the 
additive nonbonded functional form and therefore are tied to the strength of the 
1-4 interactions.  Some force fields "fudge" the 1-4 terms to compensate (in 
part) for such errors.  CHARMM does not.



Secondly, do you have any experience with QM/MM MD? Should I rescale the
1,4 interactions? I searched for that but found nothing. Perhaps I've
missed a
paper.



1-4 interactions are purely a construct of the empirical force field.  They are 
not relevant to the QM subsystem because no such empirical model exists there, 
it is QM.


-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] genion command

[Justin Lemkul]

On 5/16/17 12:55 AM, Saumyak Mukherjee wrote:

Hello Diana,

You may try using the -conc flag in genion program to specify your salt
concentration, along with -nname and -pname flags.



The -nname and -pname options are irrelevant here.

If there are fewer than 1000 waters in the system, I doubt the number of ions 
has been calculated correctly, though.  Compare with -conc 0.6 to see if the 
math is right, and make sure that the solvent is actually being replaced, not 
anything else.


-Justin


Best wishes,
Saumyak

On 16 May 2017 at 10:18, diana p  wrote:


Dear gmx users,
I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
genion command and add 720 CL and 360 Ca ions respectively to the system of
pure 12568 water molecules.But on running the command genion I get error
message:

Program genion, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c,
line:
89
Fatal error:
No more replaceable solvent!

How should I add ions in the system.I would be more than pleased if someone
could guid me.
Thank You in advance
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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] Problem in Bootstrapping of PMF

[Justin Lemkul]

On 5/16/17 7:15 AM, Alex wrote:

Hello gromacs user,

I have calculated the PMF by umbrella sampling for my system, by below
command I am trying to Bootstrap my PMF, but I do not know why bsResult.xvg
in whcih the error bars is stored can not be produced. The rests contain
Profile, bsProfs.xvg are easily be calculated though.

I increased the time and number of used 512 CPU's, but after more than one
week the bootstrapping stopped again just because of time limit with out
bsResult.xvg.

I have already done nicely the same calculation for some similar systems,
even with higher number of bins and bootstraps, and this is the only one I
have problem with in spite of the similar ingredients.

-
#$ -l h_rt=85,h_vmem=3200M
#$ -notify
#$ -cwd
#$ -A gromacs_parallel
#$ -pe orte_sl16* 512

mpirun -x PATH -np 1 gmx_mpi wham -hist Histo.xvg -nBootstrap 350
-bins 350 -bs-method b-hist -bsres bsResult.xvg -bsprof bsProfs.xvg -if
Fpull.dat -it TPR.dat -min 1.18 -max 3.6 -ac -o Profile.xvg -zprof0 3.6 -b
48000 -unit kCal >bot.log 2>&1
--

An help is highly appreciated.



Does it work if you run normally, e.g. not via mpirun?  There's nothing to gain 
here by doing this.  The latest gmx wham can use OpenMP via the OMP_NUM_THREADS 
environment variable if you want to speed things up.


-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] Fwd: Issue with parallel simulations in vacuum

[Justin Lemkul]

On 5/16/17 7:26 AM, Agusti Emperador wrote:

Dear GROMACS experts,

I am simulating a system of two disordered proteins in vacuum. I use
gromacs 4.6.5. The serial simulation works fine, but when I run it in
parallel (2 processors) it gives seriously pathological results.

I use particle decomposition and periodic boundary conditions, because I
want to simulate a solution at a certain concentration (technically, the
simulation is in vacuum, but I have included the effects of solvation in
the nonbonded terms of the force field in my coarse-grained protein model).
Each protein has 300 particles.

I use exactly the same parameters and input files in the serial simulation
and in the parallel simulation. This is the mdp file that I use:

integrator   =  md-vv
dt   =  0.02
nsteps   =  5
nstxout  =  0
nstvout  =  0
nstenergy = 50
nstlog   =  50
nstxtcout=  5
nstcomm = 1
nstcalcenergy = 1
xtc-precision=  10
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
tcoupl   =  andersen
tc-grps  =  Protein
tau-t=  .1
ref-t=  300
Pcoupl   =  no
refcoord_scaling =  all

It works perfectly in the serial simulation, but I need to make parallel
simulations in order to simulate systems with many proteins.

How could I solve the problem?



What is the problem?  What do you define as "seriously pathological results" in 
this case?  Also note that 4.6.5 is practically prehistoric and you may wish to 
consider a newer, faster, less-buggy version of the code.


-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] Graphene modeling

[Justin Lemkul]

On 5/16/17 7:31 AM, ‪Mohammad Roostaie‬ ‪ wrote:

In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa
-name CNT -noparam" and I got this error:

Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2t
There are 6 name to type translations in file ./cnt_oplsaa.ff
Generating bonds from distances...
atom 46
There are 1 different atom types in your sample
Generating angles and dihedrals from bonds...
Segmentation fault



Are you using the latest version of GROMACS?  There was an x2top seg fault fixed 
a few versions ago so using 2016.3 may be necessary here.


-Justin


Best
Mohammad



*From:* ‪Mohammad Roostaie‬ ‪ 
*To:* Justin Lemkul ; gmx-us...@gromacs.org
*Sent:* Tuesday, 16 May 2017, 13:59:29
*Subject:* Re: [gmx-users] Graphene modeling

Thank you Justin,

Actually, I want to simulate a small box of water with graphene and protein. You
mean that I should just build and put the .n2t file in the directory where I
want to run the system, and no other files are required or should not be 
changed.

I used the files specified in this
link: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube


For example, for .n2t file:

|; Oplsaa-based n2t for carbon-based structures such as CNTs and graphenes ;
Andrea Minoia H HJ 0.00 1.008 1 C 0.109 ;Hydrogen C CJ 0.00 12.011 3 C 0.142 H
0.109 H 0.109 ;Periferic C C CJ 0.00 12.011 3 C 0.142 C 0.142 H 0.108 ;Periferic
C C CJ 0.00 12.011 1 C 0.142 ;Internal/periodic C C CJ 0.00 12.011 2 C 0.142 C
0.142 ;Internal/periodic C C CJ 0.00 12.011 3 C 0.142 C 0.142 C 0.142
;Internal/periodic C|


Thanks,
Mohammad

*From:* Justin Lemkul 
*To:* gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ 
*Sent:* Monday, 15 May 2017, 16:45:19
*Subject:* Re: [gmx-users] Graphene modeling



On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi GROMACS users,



I want to model a graphene sheet. I used the instruction stated in link

http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube.
I put the
cnt_oplsaa.ff folder in the directory where I want to run the rest of the work.
Also, I rename the residues of the graphene to “CJ” and the atoms to “C”. but,
when I want to use “gmx x2top”, I get the error that says it cannot find any
forcefield type for the atoms. Can you please help me to figure this out?





Since all you have are C atoms, this should require only a one-line .n2t file
(or addition to an existing one) that specifies the proper equilibrium bond
length for C-C in your structure.  Without seeing your .n2t file and the x2top
screen output, there's nothing to suggest other than your .n2t file is somehow
inadequate for what you're trying to do.

-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


==






--
==

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] Hydroxyl bonds rotating too much

[Justin Lemkul]

On 5/16/17 7:03 AM, Juan José Galano Frutos wrote:

Hi there:

I am simulating a protein which include as a cofactor a molecule bearing
some hydroxyl groups. The system is crashing from the begining of the
equilibration step (after the following steps: vaccuum minimization,
solvating, neutralizing, minimization, heating) due to -in all the
replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
degrees.
I checked the structures and the systems looking for either water or
protein parts in so close contact with this hydroxyl groups, but it was not
the case. Then I proceeded to re-minimize again the systems after the
heating step and afterward to relaunch the equilibration step, but again
the same happened. I also checked the topology file of this cofactor but
all seems to be fine, I mean charges.
Then, what could be happening? Is it common this behaviour in hydroxyl
groups?Any help please



What does the problematic OH group interact with?  The over-rotation is a 
symptom, not a cause.  If it interacts with your cofactor, the parameters for 
that cofactor are likely suspect.  Typical diagnostic steps are in 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


-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] Perturbation Thermodynamic Integration

[Justin Lemkul]

On 5/16/17 9:53 AM, Dan Gil wrote:

Hi,

The latest version of Gromacs I have is 5.1. Using this version, grompp
produces no warnings or errors.

I am using OPLS-AA, and I didn't have any issues with it thus far. I
inherited this research project though 3 years ago. Is there something you
think I should look at with scrutiny?



The rvdw is very long (no FF uses one like that) though cutoffs for OPLS-AA vary 
paper by paper, unfortunately.  Typical values for all cutoffs are 1.0.  Your 
fourierspacing is about 3-4 times too large so your use of PME is probably 
insufficiently accurate.  Stick with the default of 0.12 to get beta ~0.34 or so.


-Justin


On Tue, May 16, 2017 at 9:42 AM, Mark Abraham 
wrote:


Hi,

Yes that looks like it is the envelope of the new warning. What does grompp
from 2016.3 report?

(Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd
reject that method immediately unless there was evidence that it worked
well for a range of observables, and was consistent with other practice for
that force field. If there is such evidence, for my information, what model
/ force field does it like that?)

Mark

On Tue, May 16, 2017 at 3:30 PM Dan Gil  wrote:


Sorry, here is the mdp file:

;Integration Method and Parameters
integrator   = sd
nsteps   = 10
dt = 0.002
nstenergy= 1000
nstlog   = 5000

;Output Control
nstxout = 0
nstvout = 0

;Cutoff Schemes
cutoff-scheme= group
rlist= 1.0
vdw-type = cut-off
rvdw = 2.0

;Coulomb interactions
coulombtype  = pme
rcoulomb = 1.0
fourierspacing   = 0.4

;Constraints
constraints  = all-bonds

;Temperature coupling
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.1
ref-t= 300

;Pressure coupling
pcoupl = parrinello-rahman
ref-p = 1.01325
compressibility = 4.5e-5
tau-p = 5

;Free energy calculation
free-energy  = yes
init-lambda-state= 8
delta-lambda = 0
fep-lambdas  =
calc-lambda-neighbors= 1
vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
couple-moltype   = HEPT
couple-lambda0   = vdwq
couple-lambda1   = none
couple-intramol  = no
nstdhdl  = 10


On Tue, May 16, 2017 at 1:02 AM, Mark Abraham 
wrote:


Hi,

What use are you making of constraints? Justin suggested sharing a full

mdp

file, which I think may help. We discovered last year that you can get
equipartition failure for (IIRC) all-bonds constraints for moieties

like

-CH2Cl, and latest grompp now detects this.

Mark

On Tue, 16 May 2017 01:16 Dan Gil  wrote:


Hello,

The last thread was getting too big, and the conversation evolved to

a

topic different from my original question, so I decided to start a

new

thread.

We were discussing thermodynamic integration, and why the

mass_lambdas

would have any contribution to the derivative of the Hamiltonian.

I found a source (link below) which derives the Gibbs free energy

change

as

a function of lambda. I learned that the mass contribution is often

assumed

to be small and negligible, given that the mass difference between

the

two

lambda states are small.
http://www.tandfonline.com/doi/abs/10.1080/00268970600893060

I think that the mass of the two lambda states that equation (14) is
referring to is the total mass (mass of solvent plus solute). My

system

is

1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder

if I

am getting nonzero mass contributions (in my dhdl.xvg output) because

of

finite-size effects? Would completely neglecting the mass

contributions

be

acceptable? Does doing this technically change the system to one that

is

1

solute and an infinite number of solvent molecules where the mass
contributions limit is zero?

Best Regards,

Dan
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Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Hi,

The latest version of Gromacs I have is 5.1. Using this version, grompp
produces no warnings or errors.

I am using OPLS-AA, and I didn't have any issues with it thus far. I
inherited this research project though 3 years ago. Is there something you
think I should look at with scrutiny?

On Tue, May 16, 2017 at 9:42 AM, Mark Abraham 
wrote:

> Hi,
>
> Yes that looks like it is the envelope of the new warning. What does grompp
> from 2016.3 report?
>
> (Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd
> reject that method immediately unless there was evidence that it worked
> well for a range of observables, and was consistent with other practice for
> that force field. If there is such evidence, for my information, what model
> / force field does it like that?)
>
> Mark
>
> On Tue, May 16, 2017 at 3:30 PM Dan Gil  wrote:
>
> > Sorry, here is the mdp file:
> >
> > ;Integration Method and Parameters
> > integrator   = sd
> > nsteps   = 10
> > dt = 0.002
> > nstenergy= 1000
> > nstlog   = 5000
> >
> > ;Output Control
> > nstxout = 0
> > nstvout = 0
> >
> > ;Cutoff Schemes
> > cutoff-scheme= group
> > rlist= 1.0
> > vdw-type = cut-off
> > rvdw = 2.0
> >
> > ;Coulomb interactions
> > coulombtype  = pme
> > rcoulomb = 1.0
> > fourierspacing   = 0.4
> >
> > ;Constraints
> > constraints  = all-bonds
> >
> > ;Temperature coupling
> > tcoupl   = v-rescale
> > tc-grps  = system
> > tau-t= 0.1
> > ref-t= 300
> >
> > ;Pressure coupling
> > pcoupl = parrinello-rahman
> > ref-p = 1.01325
> > compressibility = 4.5e-5
> > tau-p = 5
> >
> > ;Free energy calculation
> > free-energy  = yes
> > init-lambda-state= 8
> > delta-lambda = 0
> > fep-lambdas  =
> > calc-lambda-neighbors= 1
> > vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
> > coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
> > bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
> > restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
> > mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> > couple-moltype   = HEPT
> > couple-lambda0   = vdwq
> > couple-lambda1   = none
> > couple-intramol  = no
> > nstdhdl  = 10
> >
> >
> > On Tue, May 16, 2017 at 1:02 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > What use are you making of constraints? Justin suggested sharing a full
> > mdp
> > > file, which I think may help. We discovered last year that you can get
> > > equipartition failure for (IIRC) all-bonds constraints for moieties
> like
> > > -CH2Cl, and latest grompp now detects this.
> > >
> > > Mark
> > >
> > > On Tue, 16 May 2017 01:16 Dan Gil  wrote:
> > >
> > > > Hello,
> > > >
> > > > The last thread was getting too big, and the conversation evolved to
> a
> > > > topic different from my original question, so I decided to start a
> new
> > > > thread.
> > > >
> > > > We were discussing thermodynamic integration, and why the
> mass_lambdas
> > > > would have any contribution to the derivative of the Hamiltonian.
> > > >
> > > > I found a source (link below) which derives the Gibbs free energy
> > change
> > > as
> > > > a function of lambda. I learned that the mass contribution is often
> > > assumed
> > > > to be small and negligible, given that the mass difference between
> the
> > > two
> > > > lambda states are small.
> > > > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> > > >
> > > > I think that the mass of the two lambda states that equation (14) is
> > > > referring to is the total mass (mass of solvent plus solute). My
> system
> > > is
> > > > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder
> > if I
> > > > am getting nonzero mass contributions (in my dhdl.xvg output) because
> > of
> > > > finite-size effects? Would completely neglecting the mass
> contributions
> > > be
> > > > acceptable? Does doing this technically change the system to one that
> > is
> > > 1
> > > > solute and an infinite number of solvent molecules where the mass
> > > > contributions limit is zero?
> > > >
> > > > Best Regards,
> > > >
> > > > Dan
> > > > --
> > > > 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 http:/

Re: [gmx-users] Perturbation Thermodynamic Integration

[Mark Abraham]

Hi,

Yes that looks like it is the envelope of the new warning. What does grompp
from 2016.3 report?

(Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd
reject that method immediately unless there was evidence that it worked
well for a range of observables, and was consistent with other practice for
that force field. If there is such evidence, for my information, what model
/ force field does it like that?)

Mark

On Tue, May 16, 2017 at 3:30 PM Dan Gil  wrote:

> Sorry, here is the mdp file:
>
> ;Integration Method and Parameters
> integrator   = sd
> nsteps   = 10
> dt = 0.002
> nstenergy= 1000
> nstlog   = 5000
>
> ;Output Control
> nstxout = 0
> nstvout = 0
>
> ;Cutoff Schemes
> cutoff-scheme= group
> rlist= 1.0
> vdw-type = cut-off
> rvdw = 2.0
>
> ;Coulomb interactions
> coulombtype  = pme
> rcoulomb = 1.0
> fourierspacing   = 0.4
>
> ;Constraints
> constraints  = all-bonds
>
> ;Temperature coupling
> tcoupl   = v-rescale
> tc-grps  = system
> tau-t= 0.1
> ref-t= 300
>
> ;Pressure coupling
> pcoupl = parrinello-rahman
> ref-p = 1.01325
> compressibility = 4.5e-5
> tau-p = 5
>
> ;Free energy calculation
> free-energy  = yes
> init-lambda-state= 8
> delta-lambda = 0
> fep-lambdas  =
> calc-lambda-neighbors= 1
> vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
> coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
> bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
> restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
> mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> couple-moltype   = HEPT
> couple-lambda0   = vdwq
> couple-lambda1   = none
> couple-intramol  = no
> nstdhdl  = 10
>
>
> On Tue, May 16, 2017 at 1:02 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > What use are you making of constraints? Justin suggested sharing a full
> mdp
> > file, which I think may help. We discovered last year that you can get
> > equipartition failure for (IIRC) all-bonds constraints for moieties like
> > -CH2Cl, and latest grompp now detects this.
> >
> > Mark
> >
> > On Tue, 16 May 2017 01:16 Dan Gil  wrote:
> >
> > > Hello,
> > >
> > > The last thread was getting too big, and the conversation evolved to a
> > > topic different from my original question, so I decided to start a new
> > > thread.
> > >
> > > We were discussing thermodynamic integration, and why the mass_lambdas
> > > would have any contribution to the derivative of the Hamiltonian.
> > >
> > > I found a source (link below) which derives the Gibbs free energy
> change
> > as
> > > a function of lambda. I learned that the mass contribution is often
> > assumed
> > > to be small and negligible, given that the mass difference between the
> > two
> > > lambda states are small.
> > > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> > >
> > > I think that the mass of the two lambda states that equation (14) is
> > > referring to is the total mass (mass of solvent plus solute). My system
> > is
> > > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder
> if I
> > > am getting nonzero mass contributions (in my dhdl.xvg output) because
> of
> > > finite-size effects? Would completely neglecting the mass contributions
> > be
> > > acceptable? Does doing this technically change the system to one that
> is
> > 1
> > > solute and an infinite number of solvent molecules where the mass
> > > contributions limit is zero?
> > >
> > > Best Regards,
> > >
> > > Dan
> > > --
> > > 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/
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> >
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Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Sorry, here is the mdp file:

;Integration Method and Parameters
integrator   = sd
nsteps   = 10
dt = 0.002
nstenergy= 1000
nstlog   = 5000

;Output Control
nstxout = 0
nstvout = 0

;Cutoff Schemes
cutoff-scheme= group
rlist= 1.0
vdw-type = cut-off
rvdw = 2.0

;Coulomb interactions
coulombtype  = pme
rcoulomb = 1.0
fourierspacing   = 0.4

;Constraints
constraints  = all-bonds

;Temperature coupling
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.1
ref-t= 300

;Pressure coupling
pcoupl = parrinello-rahman
ref-p = 1.01325
compressibility = 4.5e-5
tau-p = 5

;Free energy calculation
free-energy  = yes
init-lambda-state= 8
delta-lambda = 0
fep-lambdas  =
calc-lambda-neighbors= 1
vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
couple-moltype   = HEPT
couple-lambda0   = vdwq
couple-lambda1   = none
couple-intramol  = no
nstdhdl  = 10


On Tue, May 16, 2017 at 1:02 AM, Mark Abraham 
wrote:

> Hi,
>
> What use are you making of constraints? Justin suggested sharing a full mdp
> file, which I think may help. We discovered last year that you can get
> equipartition failure for (IIRC) all-bonds constraints for moieties like
> -CH2Cl, and latest grompp now detects this.
>
> Mark
>
> On Tue, 16 May 2017 01:16 Dan Gil  wrote:
>
> > Hello,
> >
> > The last thread was getting too big, and the conversation evolved to a
> > topic different from my original question, so I decided to start a new
> > thread.
> >
> > We were discussing thermodynamic integration, and why the mass_lambdas
> > would have any contribution to the derivative of the Hamiltonian.
> >
> > I found a source (link below) which derives the Gibbs free energy change
> as
> > a function of lambda. I learned that the mass contribution is often
> assumed
> > to be small and negligible, given that the mass difference between the
> two
> > lambda states are small.
> > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> >
> > I think that the mass of the two lambda states that equation (14) is
> > referring to is the total mass (mass of solvent plus solute). My system
> is
> > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder if I
> > am getting nonzero mass contributions (in my dhdl.xvg output) because of
> > finite-size effects? Would completely neglecting the mass contributions
> be
> > acceptable? Does doing this technically change the system to one that is
> 1
> > solute and an infinite number of solvent molecules where the mass
> > contributions limit is zero?
> >
> > Best Regards,
> >
> > Dan
> > --
> > 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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[gmx-users] Hydroxyl bonds rotating too much

[Juan José Galano Frutos]

For more details, my system also has another cofactor with similar
characteristics (FAD), I mean with hydroxyl groups but all is going fine
with it so far (equilibration step).

As I wrote before I did the following steps:
1- vaccuum minimization
2- solvating
3- neutralizing
4- minimization
5- heating (increases by temperature ramp and using position restraints for
all the components of the system)
6- equilibration (3 sequencial steps: the first step (NVT with a v-rescale
thermostat) is where the system crashes)

here the .mdp file of this first equilibration step:

define  =

integrator  = md
dt = 0.001  ; ps !
nsteps  = 15 ; 150 ps
nstcomm  = 1
nstxtcout  = 1
xtc-precision = 1
nstxout = 0
nstvout = 0
nstfout  = 0
nstlog   = 1
nstenergy  = 1

; Non-bonded Interactions
nstlist   = 10
ns_type= grid
rlist  = 0.9
coulombtype = PME
rcoulomb  = 0.9
vdwtype   = cut-off
rvdw = 0.9
vdw-modifier = Potential-shift-Verlet

; Berendsen temperature coupling is on in two groups
Tcoupl  =  v-rescale
tc-grps =  System
tau_t=  0.1
ref_t =  310

; Energy monitoring
energygrps=  System
DispCorr=  EnerPres

; Isotropic pressure coupling is now off
Pcoupl  =  no
Pcoupltype=  isotropic
tau_p=  5.0
compressibility   =  4.6e-5
ref_p =  1.0

; Generate velocites is off at 310 K
gen_vel  =  no
gen_temp   =  310
gen_seed   =  -1

; Constraints
constraint_algorithm = lincs
lincs_order   = 8
constraints   = all-bonds
lincs-warnangle = 60
disre= simple



Thank you in advance

Best regards

Juan José




2017-05-16 13:03 GMT+02:00 Juan José Galano Frutos :

> Hi there:
>
> I am simulating a protein which include as a cofactor a molecule bearing
> some hydroxyl groups. The system is crashing from the begining of the
> equilibration step (after the following steps: vaccuum minimization,
> solvating, neutralizing, minimization, heating) due to -in all the
> replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
> degrees.
> I checked the structures and the systems looking for either water or
> protein parts in so close contact with this hydroxyl groups, but it was not
> the case. Then I proceeded to re-minimize again the systems after the
> heating step and afterward to relaunch the equilibration step, but again
> the same happened. I also checked the topology file of this cofactor but
> all seems to be fine, I mean charges.
> Then, what could be happening? Is it common this behaviour in hydroxyl
> groups?Any help please
>
> Thanks
>
> Best
>
> Juan José Galano Frutos
>
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Faculty of Sciences,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza (Spain)
> +34 976 76 28 06 <+34%20976%2076%2028%2006>
>
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
>
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Re: [gmx-users] Graphene modeling

[‪Mohammad Roostaie‬ ‪]

In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa 
-name CNT -noparam" and I got this error:
Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2tThere are 6 name to 
type translations in file ./cnt_oplsaa.ffGenerating bonds from distances...atom 
46There are 1 different atom types in your sampleGenerating angles and 
dihedrals from bonds...Segmentation fault BestMohammad 

  From: ‪Mohammad Roostaie‬ ‪ 
 To: Justin Lemkul ; gmx-us...@gromacs.org 
 Sent: Tuesday, 16 May 2017, 13:59:29
 Subject: Re: [gmx-users] Graphene modeling
   
Thank you Justin,
Actually, I want to simulate a small box of water with graphene and protein. 
You mean that I should just build and put the .n2t file in the directory where 
I want to run the system, and no other files are required or should not be 
changed. 
I used the files specified in this link: 
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
For example, for .n2t file:; Oplsaa-based n2t for carbon-based structures such 
as CNTs and graphenes
; Andrea Minoia
HHJ0.00   1.008  1C 0.109  ;Hydrogen
CCJ0.00  12.011  3C 0.142   H 0.109   H 0.109 ;Periferic C
CCJ0.00  12.011  3C 0.142   C 0.142   H 0.108 ;Periferic C
CCJ0.00  12.011  1C 0.142  
;Internal/periodic C
CCJ0.00  12.011  2C 0.142   C 0.142
;Internal/periodic C
CCJ0.00  12.011  3C 0.142   C 0.142   C 0.142 
;Internal/periodic C
Thanks,Mohammad  From: Justin Lemkul 
 To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪  
 Sent: Monday, 15 May 2017, 16:45:19
 Subject: Re: [gmx-users] Graphene modeling
  


On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi GROMACS users,
>
>
>
> I want to model a graphene sheet. I used the instruction stated in link 
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the 
> cnt_oplsaa.ff folder in the directory where I want to run the rest of the 
> work. Also, I rename the residues of the graphene to “CJ” and the atoms to 
> “C”. but, when I want to use “gmx x2top”, I get the error that says it cannot 
> find any forcefield type for the atoms. Can you please help me to figure this 
> out?
>

Since all you have are C atoms, this should require only a one-line .n2t file 
(or addition to an existing one) that specifies the proper equilibrium bond 
length for C-C in your structure.  Without seeing your .n2t file and the x2top 
screen output, there's nothing to suggest other than your .n2t file is somehow 
inadequate for what you're trying to do.

-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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[gmx-users] Fwd: Issue with parallel simulations in vacuum

[Agusti Emperador]

Dear GROMACS experts,

I am simulating a system of two disordered proteins in vacuum. I use
gromacs 4.6.5. The serial simulation works fine, but when I run it in
parallel (2 processors) it gives seriously pathological results.

I use particle decomposition and periodic boundary conditions, because I
want to simulate a solution at a certain concentration (technically, the
simulation is in vacuum, but I have included the effects of solvation in
the nonbonded terms of the force field in my coarse-grained protein model).
Each protein has 300 particles.

I use exactly the same parameters and input files in the serial simulation
and in the parallel simulation. This is the mdp file that I use:

integrator   =  md-vv
dt   =  0.02
nsteps   =  5
nstxout  =  0
nstvout  =  0
nstenergy = 50
nstlog   =  50
nstxtcout=  5
nstcomm = 1
nstcalcenergy = 1
xtc-precision=  10
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
tcoupl   =  andersen
tc-grps  =  Protein
tau-t=  .1
ref-t=  300
Pcoupl   =  no
refcoord_scaling =  all

It works perfectly in the serial simulation, but I need to make parallel
simulations in order to simulate systems with many proteins.

How could I solve the problem?

Thank you in advance,

Agusti
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[gmx-users] Problem in Bootstrapping of PMF

[Alex]

Hello gromacs user,

I have calculated the PMF by umbrella sampling for my system, by below
command I am trying to Bootstrap my PMF, but I do not know why bsResult.xvg
in whcih the error bars is stored can not be produced. The rests contain
Profile, bsProfs.xvg are easily be calculated though.

I increased the time and number of used 512 CPU's, but after more than one
week the bootstrapping stopped again just because of time limit with out
bsResult.xvg.

I have already done nicely the same calculation for some similar systems,
even with higher number of bins and bootstraps, and this is the only one I
have problem with in spite of the similar ingredients.

-
#$ -l h_rt=85,h_vmem=3200M
#$ -notify
#$ -cwd
#$ -A gromacs_parallel
#$ -pe orte_sl16* 512

mpirun -x PATH -np 1 gmx_mpi wham -hist Histo.xvg -nBootstrap 350
-bins 350 -bs-method b-hist -bsres bsResult.xvg -bsprof bsProfs.xvg -if
Fpull.dat -it TPR.dat -min 1.18 -max 3.6 -ac -o Profile.xvg -zprof0 3.6 -b
48000 -unit kCal >bot.log 2>&1
--

An help is highly appreciated.

Cheers,
Alex
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[gmx-users] Hydroxyl bonds rotating too much

[Juan José Galano Frutos]

Hi there:

I am simulating a protein which include as a cofactor a molecule bearing
some hydroxyl groups. The system is crashing from the begining of the
equilibration step (after the following steps: vaccuum minimization,
solvating, neutralizing, minimization, heating) due to -in all the
replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
degrees.
I checked the structures and the systems looking for either water or
protein parts in so close contact with this hydroxyl groups, but it was not
the case. Then I proceeded to re-minimize again the systems after the
heating step and afterward to relaunch the equilibration step, but again
the same happened. I also checked the topology file of this cofactor but
all seems to be fine, I mean charges.
Then, what could be happening? Is it common this behaviour in hydroxyl
groups?Any help please

Thanks

Best

Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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Re: [gmx-users] Unreasonably high pressure values

[Kamps, M.]

Dear Mark,

I'm sorry for being unclear. I have rectangular box (20x5x7 nm, XYZ)
where a flow should be replicated. at Z=0 and Z=7 there are two
surfaces composed of gold atoms. In between there is a fluid. The
system is open or periodic in the X and Y directions, but limited in
the Z direction by the surfaces (PBC is set to XYZ, while periodic
molecules is set to yes). Both surfaces 'connect' through the PBC. The
goal is to replicate a fluid flow between the two surfaces, which will
by done by applying a constant acceleration to the fluid in the X
direction. The flow will be therefore along the X axis. It is somewhat
similar to articles as these:
http://advances.sciencemag.org/content/2/3/e1501585/tab-pdf

I don't fully understand what you mean in your last sentences. Why
shouldn't my system produce sane values of pressure?


___


Message: 1
Date: Tue, 16 May 2017 09:11:46 +
From: Mark Abraham 
To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Unreasonably high pressure values
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Hi,

I don't understand the system very well from your description. You have two
surfaces, a fluid between them, presumably periodic in the dimensions of
the surface. But what do you have in the direction normal to the surface?
Whatever it is, why should your parameterization of your gold atoms LJ lead
to sane pressure? What do you get from a normal 3D periodic system with a
surface solvated on both sides?

Mark
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Re: [gmx-users] Graphene modeling

[‪Mohammad Roostaie‬ ‪]

Thank you Justin,
Actually, I want to simulate a small box of water with graphene and protein. 
You mean that I should just build and put the .n2t file in the directory where 
I want to run the system, and no other files are required or should not be 
changed. 
I used the files specified in this link: 
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
For example, for .n2t file:; Oplsaa-based n2t for carbon-based structures such 
as CNTs and graphenes
; Andrea Minoia
HHJ0.00   1.008  1C 0.109  ;Hydrogen
CCJ0.00  12.011  3C 0.142   H 0.109   H 0.109 ;Periferic C
CCJ0.00  12.011  3C 0.142   C 0.142   H 0.108 ;Periferic C
CCJ0.00  12.011  1C 0.142  
;Internal/periodic C
CCJ0.00  12.011  2C 0.142   C 0.142
;Internal/periodic C
CCJ0.00  12.011  3C 0.142   C 0.142   C 0.142 
;Internal/periodic C
Thanks,Mohammad  From: Justin Lemkul 
 To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪  
 Sent: Monday, 15 May 2017, 16:45:19
 Subject: Re: [gmx-users] Graphene modeling
   


On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi GROMACS users,
>
>
>
> I want to model a graphene sheet. I used the instruction stated in link 
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the 
> cnt_oplsaa.ff folder in the directory where I want to run the rest of the 
> work. Also, I rename the residues of the graphene to “CJ” and the atoms to 
> “C”. but, when I want to use “gmx x2top”, I get the error that says it cannot 
> find any forcefield type for the atoms. Can you please help me to figure this 
> out?
>

Since all you have are C atoms, this should require only a one-line .n2t file 
(or addition to an existing one) that specifies the proper equilibrium bond 
length for C-C in your structure.  Without seeing your .n2t file and the x2top 
screen output, there's nothing to suggest other than your .n2t file is somehow 
inadequate for what you're trying to do.

-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] NMA eigenvectors doubts

[luca maggi]

During the calculation of the hessian matrix (the mdrun step) gromacs  gives me 
the output:

"

There are: 127659 Atoms

Non-cutoff electrostatics used, forcing full Hessian format.

Allocating Hessian memory...


starting normal mode calculation 'Protein in water'

15904 steps.


Maximum force: 1.64976e-02

The force is probably not small enough to ensure that you are at a minimum.

Be aware that negative eigenvalues may occur

when the resulting matrix is diagonalized


Finished step 1690 out of 7952"


At this stage it comes out with this weird number...I don't konow if it could 
be helpful!

The command I used is simply:


gmx_mpi_d mdrun  -deffnm nm_calc_67 -v -ntomp 32


Best

Luca


Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 per conto di Mark Abraham 

Inviato: martedì 16 maggio 2017 10.25
A: gmx-us...@gromacs.org
Oggetto: Re: [gmx-users] NMA eigenvectors doubts

Hi,

I suggest you go back through your workflow, paying attention to any time
you selected a group of atoms for output or analysis, and reading carefully
through the outputs of the various tools. If the output isn't what you
expect... reconsider the input. :-)

Mark

On Tue, May 16, 2017 at 9:05 AM luca maggi  wrote:

> The protein atoms are  6908. I have a membrane  with 35884 atoms and water
> 84696. So far I calculated only the first eigenvector but as I said I
> can't  understand why the number of row  of this vector is 7952 or so.
>
>
> Luca
>
> 
> Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> per conto di Peter
> Stern 
> Inviato: martedì 16 maggio 2017 08.25
> A: gmx-us...@gromacs.org
> Oggetto: Re: [gmx-users] NMA eigenvectors doubts
>
> How many protein atoms do you have?  How many eigenvectors?  The program
> is not going to calculate the normal modes of the water molecules.
>
> Peter
>
> Sent from my iPhone
>
> > On May 16, 2017, at 8:53 AM, luca maggi  wrote:
> >
> > Hi Peter,
> >
> > Thanks  for your answer...but my system is composed by a protein and  a
> membrane plus the water. The  Calphas are just 438, so I don't think that
> number is referred to alpha carbons. Moreover I didn't set my calculation
> in order to calculate the  Calpha eigenvectors...
> >
> >
> >
> > 
> > Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> per conto di Peter
> Stern 
> > Inviato: lunedì 15 maggio 2017 23.14
> > A: gmx-us...@gromacs.org
> > Oggetto: Re: [gmx-users] NMA eigenvectors doubts
> >
> > Perhaps just the eigenvectors for the Calpha atoms.
> >
> > Peter
> >
> > Sent from my iPhone
> >
> > On May 15, 2017, at 9:30 PM, luca maggi  maggi_l...@hotmail.it>> wrote:
> >
> > Dear Gromacs Users,
> >
> >
> > I have performed a normal mode analysis with gromacs. I have calculated
> the hessian matrix and the related eigenvalues and eigenvectors. At this
> point  I needed to extract some elements from the  eigenvectors  and using
> the dump tool of gromacs I wrote the first of them in a file, but I
> realised something unexpected. The vector is composed by 7952 row and three
> columns. My system is composed by about 127000 atoms, thus I expected to
> find a vector with 127000 x 3 entries...but this number (7952) does not fit
> at all with my expectation. It seems to be related with the number of steps
> performed during the normal mode analysis but i cannot understand why
> >
> > How has this vector been calculated ?
> >
> >
> > Suggestion and hints would be really appreciated!!
> >
> >
> > Thanks
> >
> >
> > Luca
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
GMX-Users List - 
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This is the main discussion forum for users of GROMACS and related software. 
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Re: [gmx-users] Unreasonably high pressure values

[Mark Abraham]

Hi,

I don't understand the system very well from your description. You have two
surfaces, a fluid between them, presumably periodic in the dimensions of
the surface. But what do you have in the direction normal to the surface?
Whatever it is, why should your parameterization of your gold atoms LJ lead
to sane pressure? What do you get from a normal 3D periodic system with a
surface solvated on both sides?

Mark

On Tue, May 16, 2017 at 11:04 AM Kamps, M.  wrote:

> Dear Mark,
>
> Thanks for your answer. I did some experiments and I think I've
> located the problem.
> Within my simulation there are two main components: Two surfaces and a
> polymer fluid. These two surfaces are created by placing gold atoms in
> a FCC lattice (lattice parameters derived from the LJ potential). The
> only interactions between these surfaces are the LJ potentials.
>
> When I run a simple NVT equilibrium on a basic system (without
> pressure, without accelerations, etc), the pressure is already really
> high (again, around 6000 bar, it stabilizes around this value!). When
> I run the same NVT equilibrium on only the fluid (so no surfaces), the
> pressure remains stable at around 0-1 bar, as should be expected.
>
> Performing an NPT equilibrium after this first one grants the same
> results. The system with the surfaces shows unreasonably high pressure
> values, while the fluid-only system behaves as expected. (The
> pressures are calculated via gmx energy)
>
> My guess, the problem is related to the gold surfaces. However, when
> running only a NVT and NPT equilibration on the surfaces, nothing
> happens. There are no high stresses within the system, everything runs
> fine. The only difference is the pressure, which is extremely high.
>
> Is there a way to exclude the surface from the calculations? I am only
> interested in the LJ behaviour of the surface towards the fluid. I
> cannot use the GROMACS walls options since I am interested in non-flat
> surface.
>
> Any ideas?
>
> ___
>
> Message: 1
> Date: Mon, 15 May 2017 16:35:56 +
> From: Mark Abraham 
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Unreasonably high pressure values
> Message-ID:
>  
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> Convergence times depend on system type and size, of course, but an
> equilibration on an inhomogeneous system should probably run for more than
> a few nanoseconds. That might help expose whether the issue is the system,
> or the protocol, or the applied force.
>
> Mark
>
> On Mon, 15 May 2017 18:25 Kamps, M.  wrote:
>
> > Dear GMX users,
> >
> > I am struggling with understanding my systems behaviour.
> > I have a semi-isotropic system where my bottom and upper plane are
> > composed of gold FCC plates. In between is a fluid, which during
> > equilibration is stationary (no acceleration). I equilibrate the
> > system with a Berendsen barostat, as the literature suggests. The
> > compressibility is that of the fluid used (Hexadecane C16H34), while
> > the reference pressure is 1 bar. See the below section of my systems
> > MDP:
> >
> > ; Pressure coupling is on
> > pcoupl= berendsen; Pressure coupling on
> > pcoupltype= semiisotropic; uniform scaling
> > of box vectors
> > tau_p= 2.0; time constant, in ps
> > ref_p= 1.0 1.0; reference pressure,
> in
> > bar
> > compressibility = 0  8.6e-5; isothermal
> > compressibility, bar^-1
> >
> > When I equilibrate the system, everything appears to be normal. The
> > volume shrinks a little to compress the fluid, which leads to a
> > correct density (correct as in corresponding with known values of the
> > real-life density). The fluid behaves as expected and everything looks
> > good.
> >
> > I then want to use the system to accelerate the fluid, however that
> > blows up the system. Blowing up as in; fluctuations in the box size,
> > shrink, expand, rapid shrink, rapid expand, extreme shrink, blowing
> > up.
> >
> > Upon inspection, during equilibrating the pressure of my system nicely
> > converges, however, it converges to -6000 bar, which seems rather
> > strange.. How does this happen? What am I doing wrong?
> >
> > I use a 0.5 fs timestep, equilibriate over 400.000 steps (0.2 ns),
> > 300K v-rescale temperature coupling, PME electrostatic calculations.
> >
> > Kind regards,
> > Mark
> --
> 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] Unreasonably high pressure values

[Kamps, M.]

Dear Mark,

Thanks for your answer. I did some experiments and I think I've
located the problem.
Within my simulation there are two main components: Two surfaces and a
polymer fluid. These two surfaces are created by placing gold atoms in
a FCC lattice (lattice parameters derived from the LJ potential). The
only interactions between these surfaces are the LJ potentials.

When I run a simple NVT equilibrium on a basic system (without
pressure, without accelerations, etc), the pressure is already really
high (again, around 6000 bar, it stabilizes around this value!). When
I run the same NVT equilibrium on only the fluid (so no surfaces), the
pressure remains stable at around 0-1 bar, as should be expected.

Performing an NPT equilibrium after this first one grants the same
results. The system with the surfaces shows unreasonably high pressure
values, while the fluid-only system behaves as expected. (The
pressures are calculated via gmx energy)

My guess, the problem is related to the gold surfaces. However, when
running only a NVT and NPT equilibration on the surfaces, nothing
happens. There are no high stresses within the system, everything runs
fine. The only difference is the pressure, which is extremely high.

Is there a way to exclude the surface from the calculations? I am only
interested in the LJ behaviour of the surface towards the fluid. I
cannot use the GROMACS walls options since I am interested in non-flat
surface.

Any ideas?

___

Message: 1
Date: Mon, 15 May 2017 16:35:56 +
From: Mark Abraham 
To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Unreasonably high pressure values
Message-ID:
 
Content-Type: text/plain; charset="UTF-8"

Hi,

Convergence times depend on system type and size, of course, but an
equilibration on an inhomogeneous system should probably run for more than
a few nanoseconds. That might help expose whether the issue is the system,
or the protocol, or the applied force.

Mark

On Mon, 15 May 2017 18:25 Kamps, M.  wrote:

> Dear GMX users,
>
> I am struggling with understanding my systems behaviour.
> I have a semi-isotropic system where my bottom and upper plane are
> composed of gold FCC plates. In between is a fluid, which during
> equilibration is stationary (no acceleration). I equilibrate the
> system with a Berendsen barostat, as the literature suggests. The
> compressibility is that of the fluid used (Hexadecane C16H34), while
> the reference pressure is 1 bar. See the below section of my systems
> MDP:
>
> ; Pressure coupling is on
> pcoupl= berendsen; Pressure coupling on
> pcoupltype= semiisotropic; uniform scaling
> of box vectors
> tau_p= 2.0; time constant, in ps
> ref_p= 1.0 1.0; reference pressure, in
> bar
> compressibility = 0  8.6e-5; isothermal
> compressibility, bar^-1
>
> When I equilibrate the system, everything appears to be normal. The
> volume shrinks a little to compress the fluid, which leads to a
> correct density (correct as in corresponding with known values of the
> real-life density). The fluid behaves as expected and everything looks
> good.
>
> I then want to use the system to accelerate the fluid, however that
> blows up the system. Blowing up as in; fluctuations in the box size,
> shrink, expand, rapid shrink, rapid expand, extreme shrink, blowing
> up.
>
> Upon inspection, during equilibrating the pressure of my system nicely
> converges, however, it converges to -6000 bar, which seems rather
> strange.. How does this happen? What am I doing wrong?
>
> I use a 0.5 fs timestep, equilibriate over 400.000 steps (0.2 ns),
> 300K v-rescale temperature coupling, PME electrostatic calculations.
>
> Kind regards,
> Mark
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Re: [gmx-users] NMA eigenvectors doubts

[luca maggi]

Thanks Mark.. I am going to check all the input from the normal mode 
calculation.


Luca



Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 per conto di Mark Abraham 

Inviato: martedì 16 maggio 2017 10.25
A: gmx-us...@gromacs.org
Oggetto: Re: [gmx-users] NMA eigenvectors doubts

Hi,

I suggest you go back through your workflow, paying attention to any time
you selected a group of atoms for output or analysis, and reading carefully
through the outputs of the various tools. If the output isn't what you
expect... reconsider the input. :-)

Mark

On Tue, May 16, 2017 at 9:05 AM luca maggi  wrote:

> The protein atoms are  6908. I have a membrane  with 35884 atoms and water
> 84696. So far I calculated only the first eigenvector but as I said I
> can't  understand why the number of row  of this vector is 7952 or so.
>
>
> Luca
>
> 
> Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> per conto di Peter
> Stern 
> Inviato: martedì 16 maggio 2017 08.25
> A: gmx-us...@gromacs.org
> Oggetto: Re: [gmx-users] NMA eigenvectors doubts
>
> How many protein atoms do you have?  How many eigenvectors?  The program
> is not going to calculate the normal modes of the water molecules.
>
> Peter
>
> Sent from my iPhone
>
> > On May 16, 2017, at 8:53 AM, luca maggi  wrote:
> >
> > Hi Peter,
> >
> > Thanks  for your answer...but my system is composed by a protein and  a
> membrane plus the water. The  Calphas are just 438, so I don't think that
> number is referred to alpha carbons. Moreover I didn't set my calculation
> in order to calculate the  Calpha eigenvectors...
> >
> >
> >
> > 
> > Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> per conto di Peter
> Stern 
> > Inviato: lunedì 15 maggio 2017 23.14
> > A: gmx-us...@gromacs.org
> > Oggetto: Re: [gmx-users] NMA eigenvectors doubts
> >
> > Perhaps just the eigenvectors for the Calpha atoms.
> >
> > Peter
> >
> > Sent from my iPhone
> >
> > On May 15, 2017, at 9:30 PM, luca maggi  maggi_l...@hotmail.it>> wrote:
> >
> > Dear Gromacs Users,
> >
> >
> > I have performed a normal mode analysis with gromacs. I have calculated
> the hessian matrix and the related eigenvalues and eigenvectors. At this
> point  I needed to extract some elements from the  eigenvectors  and using
> the dump tool of gromacs I wrote the first of them in a file, but I
> realised something unexpected. The vector is composed by 7952 row and three
> columns. My system is composed by about 127000 atoms, thus I expected to
> find a vector with 127000 x 3 entries...but this number (7952) does not fit
> at all with my expectation. It seems to be related with the number of steps
> performed during the normal mode analysis but i cannot understand why
> >
> > How has this vector been calculated ?
> >
> >
> > Suggestion and hints would be really appreciated!!
> >
> >
> > Thanks
> >
> >
> > Luca
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
GMX-Users List - 
Gromacs
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This is the main discussion forum for users of GROMACS and related software. 
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This is the main discussion forum for users of GROMACS and related software. 
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funding support from the European Union Horizon 2020 Programme, the European 
Research Council ...



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Re: [gmx-users] NMA eigenvectors doubts

[Mark Abraham]

Hi,

I suggest you go back through your workflow, paying attention to any time
you selected a group of atoms for output or analysis, and reading carefully
through the outputs of the various tools. If the output isn't what you
expect... reconsider the input. :-)

Mark

On Tue, May 16, 2017 at 9:05 AM luca maggi  wrote:

> The protein atoms are  6908. I have a membrane  with 35884 atoms and water
> 84696. So far I calculated only the first eigenvector but as I said I
> can't  understand why the number of row  of this vector is 7952 or so.
>
>
> Luca
>
> 
> Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> per conto di Peter
> Stern 
> Inviato: martedì 16 maggio 2017 08.25
> A: gmx-us...@gromacs.org
> Oggetto: Re: [gmx-users] NMA eigenvectors doubts
>
> How many protein atoms do you have?  How many eigenvectors?  The program
> is not going to calculate the normal modes of the water molecules.
>
> Peter
>
> Sent from my iPhone
>
> > On May 16, 2017, at 8:53 AM, luca maggi  wrote:
> >
> > Hi Peter,
> >
> > Thanks  for your answer...but my system is composed by a protein and  a
> membrane plus the water. The  Calphas are just 438, so I don't think that
> number is referred to alpha carbons. Moreover I didn't set my calculation
> in order to calculate the  Calpha eigenvectors...
> >
> >
> >
> > 
> > Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> per conto di Peter
> Stern 
> > Inviato: lunedì 15 maggio 2017 23.14
> > A: gmx-us...@gromacs.org
> > Oggetto: Re: [gmx-users] NMA eigenvectors doubts
> >
> > Perhaps just the eigenvectors for the Calpha atoms.
> >
> > Peter
> >
> > Sent from my iPhone
> >
> > On May 15, 2017, at 9:30 PM, luca maggi  maggi_l...@hotmail.it>> wrote:
> >
> > Dear Gromacs Users,
> >
> >
> > I have performed a normal mode analysis with gromacs. I have calculated
> the hessian matrix and the related eigenvalues and eigenvectors. At this
> point  I needed to extract some elements from the  eigenvectors  and using
> the dump tool of gromacs I wrote the first of them in a file, but I
> realised something unexpected. The vector is composed by 7952 row and three
> columns. My system is composed by about 127000 atoms, thus I expected to
> find a vector with 127000 x 3 entries...but this number (7952) does not fit
> at all with my expectation. It seems to be related with the number of steps
> performed during the normal mode analysis but i cannot understand why
> >
> > How has this vector been calculated ?
> >
> >
> > Suggestion and hints would be really appreciated!!
> >
> >
> > Thanks
> >
> >
> > Luca
> > --
> > 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] NMA eigenvectors doubts

[luca maggi]

The protein atoms are  6908. I have a membrane  with 35884 atoms and water 
84696. So far I calculated only the first eigenvector but as I said I can't  
understand why the number of row  of this vector is 7952 or so.


Luca


Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 per conto di Peter Stern 

Inviato: martedì 16 maggio 2017 08.25
A: gmx-us...@gromacs.org
Oggetto: Re: [gmx-users] NMA eigenvectors doubts

How many protein atoms do you have?  How many eigenvectors?  The program is not 
going to calculate the normal modes of the water molecules.

Peter

Sent from my iPhone

> On May 16, 2017, at 8:53 AM, luca maggi  wrote:
>
> Hi Peter,
>
> Thanks  for your answer...but my system is composed by a protein and  a 
> membrane plus the water. The  Calphas are just 438, so I don't think that 
> number is referred to alpha carbons. Moreover I didn't set my calculation in 
> order to calculate the  Calpha eigenvectors...
>
>
>
> 
> Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  per conto di Peter Stern 
> 
> Inviato: lunedì 15 maggio 2017 23.14
> A: gmx-us...@gromacs.org
> Oggetto: Re: [gmx-users] NMA eigenvectors doubts
>
> Perhaps just the eigenvectors for the Calpha atoms.
>
> Peter
>
> Sent from my iPhone
>
> On May 15, 2017, at 9:30 PM, luca maggi 
> mailto:maggi_l...@hotmail.it>> wrote:
>
> Dear Gromacs Users,
>
>
> I have performed a normal mode analysis with gromacs. I have calculated the 
> hessian matrix and the related eigenvalues and eigenvectors. At this point  I 
> needed to extract some elements from the  eigenvectors  and using the dump 
> tool of gromacs I wrote the first of them in a file, but I realised something 
> unexpected. The vector is composed by 7952 row and three columns. My system 
> is composed by about 127000 atoms, thus I expected to find a vector with 
> 127000 x 3 entries...but this number (7952) does not fit at all with my 
> expectation. It seems to be related with the number of steps performed during 
> the normal mode analysis but i cannot understand why
>
> How has this vector been calculated ?
>
>
> Suggestion and hints would be really appreciated!!
>
>
> Thanks
>
>
> Luca
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
GMX-Users List - 
Gromacs
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The development of Gromacs would not have been possible without generous 
funding support from the European Union Horizon 2020 Programme, the European 
Research Council ...



> This is the main discussion forum for users of GROMACS and related software. 
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