[gmx-users] segmentation fault in equilibrium

[sara soleimanzadegan]

Dear Justin,

Thank you from your response.
No, there is not any warning from grompp.
What is your idea?

Best Regards
Sara



On Friday, November 13, 2015 1:02 AM, Justin Lemkul  wrote:



On 11/12/15 10:49 AM, mohammad agha wrote:
> Dear Gromacs users,
>
> I have one system consists 150 surfactants and 14000 solvent molecules and 
> 200 water molecules by martini force field.
> When I want to reach my system to equlibrium with "mdrun pr", it isn't run 
> and I have segmentation fault. Why is it and what is the solution for this 
> problem?
>

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

Make sure you're not ignoring useful warnings from grompp.

-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] Tabulated potential error

[Pallavi Banerjee]

Hello all,

I am carrying out Iterative Boltzmann inversion on a polymer-water system.
I provide tabulated bond, angle, dihedral and a selected few non-bonded
interactions as input in the tabulated format. After only a few md steps, I
get the following error:

 A tabulated bond interaction table number 1 is out of the table range: r
2.648816, between table indices 1324 and 1325, table length 1251

What could be done to circumvent this issue?

Many Thanks

-Pallavi Banerjee
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[gmx-users] AIREBO and multibody non-bonded potentials in GROMACS

[Peter Kroon]

Dear list,

I need to model disulfide exchange reactions in an efficient way. A
literature search turned up the AIREBO formalism postulated by Brenner
at al[1]. I would like to implement this in Gromacs 5.1 as a non-bonded
functional form which has an angle dependence. So, my questions:
1) Has anybody on this list already implemented a multibody non-bonded
potential in Gromacs who would be willing to share his/her implementation?
2) What would be the best way to implement this? I will probably need to
implement both the functional itself, as well as parsing the new
topology parameters.
3) Are there any fundamental problems with using multi-body potentials
that I need to be aware of?

Thanks in advance,
Peter

[1] DOI: 10.1088/0953-8984/14/4/312


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[gmx-users] Center of mass removal for a trajectory which is already created

[Faezeh Pousaneh]

Hi,

Please some one help me how to remove center of mass motion in a trajectory
which is already created without  this setting? is that possible?

thanks in advance,

Best regards
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[gmx-users] Multiple time step MD

[Joan Clark Nicolas]

Dear gmx users,
I would be interested in running MD calculations using multiple time step
integration as described in
http://onlinelibrary.wiley.com/doi/10.1002/wcms.3/abstract .

I have searched for documentation about it but everything I have found so
far is a post from 2010 saying that the core developers were not much
interested. Is there any chance that they have changed their mind since
then?

Thanks!

PS: I have tried using Virtual Sites as well, but it becomes troublesome
when running MD on protein-ligand complexes...

*Joan Clark i Nicolas*
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Re: [gmx-users] Multiple time step MD

[Joan Clark Nicolas]

Ok, thanks!
On 13 Nov 2015 18:23, "Mark Abraham"  wrote:

> Hi,
>
> Not yet. There's some interest around, but the MD loop is pretty much a
> disaster zone at this time...
>
> Mark
>
> On Fri, 13 Nov 2015 18:31 Joan Clark Nicolas 
> wrote:
>
> > Dear gmx users,
> > I would be interested in running MD calculations using multiple time step
> > integration as described in
> > http://onlinelibrary.wiley.com/doi/10.1002/wcms.3/abstract .
> >
> > I have searched for documentation about it but everything I have found so
> > far is a post from 2010 saying that the core developers were not much
> > interested. Is there any chance that they have changed their mind since
> > then?
> >
> > Thanks!
> >
> > PS: I have tried using Virtual Sites as well, but it becomes troublesome
> > when running MD on protein-ligand complexes...
> >
> > *Joan Clark i Nicolas*
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] Multiple time step MD

[Mark Abraham]

Hi,

Not yet. There's some interest around, but the MD loop is pretty much a
disaster zone at this time...

Mark

On Fri, 13 Nov 2015 18:31 Joan Clark Nicolas  wrote:

> Dear gmx users,
> I would be interested in running MD calculations using multiple time step
> integration as described in
> http://onlinelibrary.wiley.com/doi/10.1002/wcms.3/abstract .
>
> I have searched for documentation about it but everything I have found so
> far is a post from 2010 saying that the core developers were not much
> interested. Is there any chance that they have changed their mind since
> then?
>
> Thanks!
>
> PS: I have tried using Virtual Sites as well, but it becomes troublesome
> when running MD on protein-ligand complexes...
>
> *Joan Clark i Nicolas*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] produce the surfactant.itp file

[mahdiyeh poorsargol]

Dear Gromacs users,
I'm a beginner in Gromacs and I want to work with surfactant.
I studied the tutorial 1 and 2 website for make the topology file,
but I don't know how
 produce the surfactant.itp file (for example SDS surfactant)! what's
the command
line for SDS.pdb to SDS.itp and what are its steps? please help me.
thankyou
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[gmx-users] Re : Tabulated potential error

[Pallavi Banerjee]

Hi Mark,

The maximum bond distance provided in the table_b1.xvg file is 2.5 nm. I
would guess pbc is the culprit here?
2.5 nm is already much greater than the maximum of the atomistic bond
distribution. I don't know what's going wrong.

When I carry out the very same process with a system of 1 polymer chain in
water, this error doesn't occur , but when my system has 15 polymer chains
in water, the error immediately pops up.

Any suggestions?

Many Thanks!

-Pallavi Banerjee
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Re: [gmx-users] Tabulated potential error

[Mark Abraham]

Hi,

Why do think you have a particle 2.6nm from another interacting with it?

Mark

On Fri, Nov 13, 2015 at 11:06 AM Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in> wrote:

> Hello all,
>
> I am carrying out Iterative Boltzmann inversion on a polymer-water system.
> I provide tabulated bond, angle, dihedral and a selected few non-bonded
> interactions as input in the tabulated format. After only a few md steps, I
> get the following error:
>
>  A tabulated bond interaction table number 1 is out of the table range: r
> 2.648816, between table indices 1324 and 1325, table length 1251
>
> What could be done to circumvent this issue?
>
> Many Thanks
>
> -Pallavi Banerjee
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Re : Tabulated potential error

[Mark Abraham]

Hi,

I would guess your (representation of) your interactions is to blame, e.g.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Tabulated representations of interactions work fine with PBC, and your
simplifying check with 1 polymer chain suggests the polymer-polymer
interactions are not right. You might also try two isolated polymers in a
large box.

Mark

On Fri, Nov 13, 2015 at 11:41 AM Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in> wrote:

> Hi Mark,
>
> The maximum bond distance provided in the table_b1.xvg file is 2.5 nm. I
> would guess pbc is the culprit here?
> 2.5 nm is already much greater than the maximum of the atomistic bond
> distribution. I don't know what's going wrong.
>
> When I carry out the very same process with a system of 1 polymer chain in
> water, this error doesn't occur , but when my system has 15 polymer chains
> in water, the error immediately pops up.
>
> Any suggestions?
>
> Many Thanks!
>
> -Pallavi Banerjee
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] Center of mass removal for a trajectory which is already created

[Faezeh Pousaneh]

Justin, thanks for comment.
In fact I am going to analyze g_density, but I see center of mass moves. I
have two-component system which has phase separated after a very long time.
I can't redo the simulation.
I could not mange that by tajconv.
Can I take the final .gro file of current simulation and run it with COM
removal to collect density?


Best regards


On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul  wrote:

>
>
> On 11/13/15 4:06 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> Please some one help me how to remove center of mass motion in a
>> trajectory
>> which is already created without  this setting? is that possible?
>>
>>
> Not using COM motion removal during the run leads to artifacts; no amount
> of post-processing will fix that.  If you're just looking to re-center some
> molecule(s) of interest, that's what trjconv is for.
>
> -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] segmentation fault in equilibrium

[Justin Lemkul]

On 11/13/15 3:01 AM, sara soleimanzadegan wrote:


Dear Justin,

Thank you from your response.
No, there is not any warning from grompp.
What is your idea?



Read the link I provided. Everything I would say is listed there.

-Justin


Best Regards
Sara



On Friday, November 13, 2015 1:02 AM, Justin Lemkul  wrote:



On 11/12/15 10:49 AM, mohammad agha wrote:

Dear Gromacs users,

I have one system consists 150 surfactants and 14000 solvent molecules and 200 
water molecules by martini force field.
When I want to reach my system to equlibrium with "mdrun pr", it isn't run and 
I have segmentation fault. Why is it and what is the solution for this problem?



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

Make sure you're not ignoring useful warnings from grompp.

-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] Center of mass removal for a trajectory which is already created

[Justin Lemkul]

On 11/13/15 4:06 AM, Faezeh Pousaneh wrote:

Hi,

Please some one help me how to remove center of mass motion in a trajectory
which is already created without  this setting? is that possible?



Not using COM motion removal during the run leads to artifacts; no amount of 
post-processing will fix that.  If you're just looking to re-center some 
molecule(s) of interest, that's what trjconv is for.


-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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