[gmx-users] GROMACS 5.0.7 released

[Mark Abraham]

Hi GROMACS users,

The official release of GROMACS 5.0.7 is available! It contains a few fixes
to mdrun (which are either minor in consequence or rare in occurrence), and
analysis tools. Please see the link to the release notes below for more
details. There are also some new warnings and documentation fixes. We
encourage all users to upgrade their installations from earlier 5.0
releases.

This is the last planned release in the 5.0 series. We will only make a
release of 5.0.8 if a serious issue of scientific correctness is identified
and fixed. Naturally, we will continue to make regular bug-fix releases in
the 5.1 series.

You can find the code, manual, release notes, installation instructions and
test suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.7.tar.gz
ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x/v5.0.7
http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
http://gerrit.gromacs.org/download/regressiontests-5.0.7.tar.gz

Happy simulating!

Mark Abraham
GROMACS development manager
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Re: [gmx-users] Position Restraints problem

[Mark Abraham]

Hi,

Sounds completely normal. Please see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Wed, Oct 14, 2015 at 3:08 PM Chiara Bello  wrote:

> Hi, I'm trying to apply the positions restraints only on alpha helices of
> my protein but after running mdrun, when I open the output pdb file using
> vmd, the protein appear broken: there are some atoms of the not restrained
> residues, that have been separated from the protein.
> My simulation is in implicit solvent, I have used Charm27 and
>
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Re: [gmx-users] Normal Mode Analysis

[Vitaly V. Chaban]

Perhaps, trjconv -- to delete all you do not need?







On Wed, Oct 14, 2015 at 2:49 PM, Dan Sponseller  wrote:

> Hello.
>
> I am trying to do a Normal Mode Analysis of a polymer in water. I am
> running my minimization right now with -DFLEXIBLE defined.
>
> How do I exclude the water from the analysis. I only want the analysis
> done on the polymer.
>
> Dan Sponseller
> PhD student, George Mason University
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Re: [gmx-users] when will q4md-forcefieldtools.org be back

[Mark Abraham]

Hi,

I suggest you email the people who published it, rather than repeatedly
email here. Apparently those people are not reading this list.

Mark

On Wed, Oct 14, 2015 at 8:20 PM li he  wrote:

> Dear gxmers,
> q4md-forcefieldtools.org is very important for my current project,
> but has been down for 2 weeks. Does any one has idea when will
> this website be back?
> Thank you so much~
> yours
> bob
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Re: [gmx-users] Artificial Restraint/Wall/Potential at box top

[Mark Abraham]

Hi,

You may want to consider the flat-bottomed position restraints in GROMACS 5
and up.

Mark

On Wed, Oct 14, 2015 at 8:26 PM shivangi nangia 
wrote:

> Hello,
>
> I have a system that contains 2000 CG POPC and 100 (21 AA) peptides.
>
> I want to apply  a dummy wall at the top of the box so that my peptides do
> not jump out of the box via PBC and re-enter the box from the bottom and
> stick to the bilayer.
>
> Is there a way to do that in GROMACS? distance restraint?
>
>
> Kindly suggest.
>
> Thanks in advance,
> sxn
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[gmx-users] Normal Mode Analysis

[Dan Sponseller]

Hello.

I am trying to do a Normal Mode Analysis of a polymer in water. I am running my 
minimization right now with -DFLEXIBLE defined.

How do I exclude the water from the analysis. I only want the analysis done on 
the polymer.

Dan Sponseller
PhD student, George Mason University
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[gmx-users] when will q4md-forcefieldtools.org be back

[li he]

Dear gxmers,
q4md-forcefieldtools.org is very important for my current project,
but has been down for 2 weeks. Does any one has idea when will
this website be back?
Thank you so much~
yours
bob
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[gmx-users] -gpu_id option with more than 10 GPUs

[Robert McGibbon]

Hi all,

Is there any way to use the mdrun -gpu_id option to set the PP rank to GPU
mapping on a system with more than 10 GPUs per node? IIUC, the
delimiter-free format string makes it impossible to pass gpuids of 10 or
larger.

-Robert
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Re: [gmx-users] Amber03 parameters for PTR

[Justin Lemkul]

On 10/14/15 5:02 AM, Amali Guruge wrote:

Dear All,

I want to do a molecular dynamic simulation for pdb ID 1K4T crystal
structure using Amber03 force field. The structure contains phosphotyrosine
(PTR). But parameters for PTR is not available in aminoacids.rtp file.
Therefore can anyone help me to solve my problem.



http://sites.pharmacy.manchester.ac.uk/bryce/amber

-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] Amber03 parameters for PTR

[Justin Lemkul]

On 10/14/15 5:52 AM, Amali Guruge wrote:

Dear Prof. Justin,

Thank you for the reply. Yes, I can use the parameters defined in that
site, but I have to define the aminoacids.hbd file as well for PTR. How can
I get that part?



Read the manual, and copy most of the existing entry for TYR.

-Justin


Thank you.

On Wed, Oct 14, 2015 at 3:16 PM, Justin Lemkul  wrote:




On 10/14/15 5:02 AM, Amali Guruge wrote:


Dear All,

I want to do a molecular dynamic simulation for pdb ID 1K4T crystal
structure using Amber03 force field. The structure contains
phosphotyrosine
(PTR). But parameters for PTR is not available in aminoacids.rtp file.
Therefore can anyone help me to solve my problem.



http://sites.pharmacy.manchester.ac.uk/bryce/amber

-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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[gmx-users] Amber03 parameters for PTR

[Amali Guruge]

Dear All,

I want to do a molecular dynamic simulation for pdb ID 1K4T crystal
structure using Amber03 force field. The structure contains phosphotyrosine
(PTR). But parameters for PTR is not available in aminoacids.rtp file.
Therefore can anyone help me to solve my problem.

Thank you.
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Re: [gmx-users] Amber03 parameters for PTR

[Amali Guruge]

Dear Prof. Justin,

Thank you for the reply. Yes, I can use the parameters defined in that
site, but I have to define the aminoacids.hbd file as well for PTR. How can
I get that part?

Thank you.

On Wed, Oct 14, 2015 at 3:16 PM, Justin Lemkul  wrote:

>
>
> On 10/14/15 5:02 AM, Amali Guruge wrote:
>
>> Dear All,
>>
>> I want to do a molecular dynamic simulation for pdb ID 1K4T crystal
>> structure using Amber03 force field. The structure contains
>> phosphotyrosine
>> (PTR). But parameters for PTR is not available in aminoacids.rtp file.
>> Therefore can anyone help me to solve my problem.
>>
>>
> http://sites.pharmacy.manchester.ac.uk/bryce/amber
>
> -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] What is Mnbf/s?

[Andrew DeYoung]

Hi,

I feel like this has probably been asked and answered before, but I can't
seem to find it.  Even if I Google for Mnbf/s, I can't seem to find a
definition.

In the .log output, what is Mnbf/s?

Thanks so much for your time,
Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Artificial Restraint/Wall/Potential at box top

[Vitaly V. Chaban]

Is it not better to post-process the trajectory, trjconv, to obtain the
bilayer where you need it?

Restraints impact the simulation results and this impact is not always easy
to isolate.




On Wed, Oct 14, 2015 at 3:34 PM, Mark Abraham 
wrote:

> Hi,
>
> You may want to consider the flat-bottomed position restraints in GROMACS 5
> and up.
>
> Mark
>
> On Wed, Oct 14, 2015 at 8:26 PM shivangi nangia  >
> wrote:
>
> > Hello,
> >
> > I have a system that contains 2000 CG POPC and 100 (21 AA) peptides.
> >
> > I want to apply  a dummy wall at the top of the box so that my peptides
> do
> > not jump out of the box via PBC and re-enter the box from the bottom and
> > stick to the bilayer.
> >
> > Is there a way to do that in GROMACS? distance restraint?
> >
> >
> > Kindly suggest.
> >
> > Thanks in advance,
> > sxn
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] What is Mnbf/s?

[Mark Abraham]

Hi,

Such a natural metric as "millions of non-bonded function evaluations per
second" even needs no documentation in the code, either ;-)

Mark

On Wed, Oct 14, 2015 at 10:10 PM Andrew DeYoung 
wrote:

> Hi,
>
> I feel like this has probably been asked and answered before, but I can't
> seem to find it.  Even if I Google for Mnbf/s, I can't seem to find a
> definition.
>
> In the .log output, what is Mnbf/s?
>
> Thanks so much for your time,
> Andrew DeYoung
> Carnegie Mellon University
>
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Re: [gmx-users] [gmx-developers] DNA is one moltype or two moltype?

[Erik Marklund]

Hi,

This is a user question, not a developer question, so I reply too the user list.

Normally, they do not have bonded interactions between them. And unless they 
have identical sequence, they are two molecule types.

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 14 Oct 2015, at 10:49, toannt  wrote:
> 
> 
> Hi all
> 
> I've just started to look at libgromacs for a custom simulation. I'm studying 
> the gmx data structures to initialize them directly. I wonder if molecules 
> such as DNA is considered by gromacs to be two molecule types (one for each 
> strand) or is only one molecule type with some custom-bonds between the two 
> strands?
> 
> Thanks
> 
> Toan
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Re: [gmx-users] -gpu_id option with more than 10 GPUs

[Szilárd Páll]

Hi Robert,

Just for curiosity, how do you use more than 10 GPUs? :)
What kind of CPU are you using that can handle the CPU-side load and keep
up with so many accelerators? Perhaps you are not running PME simulations?

Cheers,
--
Szilárd

On Wed, Oct 14, 2015 at 8:34 AM, Robert McGibbon  wrote:

> Hi all,
>
> Is there any way to use the mdrun -gpu_id option to set the PP rank to GPU
> mapping on a system with more than 10 GPUs per node? IIUC, the
> delimiter-free format string makes it impossible to pass gpuids of 10 or
> larger.
>
> -Robert
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Re: [gmx-users] Regarding non-bonded parameter of Zn-His for gromos96 53a6 ff

[Justin Lemkul]

On 10/14/15 8:11 AM, Navneet Chaturvedi wrote:

Dear gmx user

I need help regarding changing the unit. I found a table in article (
http://pubs.acs.org/doi/abs/10.1021/jp501737x). There are some non bonded
parameters of metal ion given in *Ai* [kcal 1/2 mol −1/2 Å−6 ] and *Bi*
[kcal 1/2 mol −1/2 Å−3 ] unit. I want to use these values in c12 and c6
values (in case of amber ff sigma and epsilon).



https://en.wikipedia.org/wiki/Lennard-Jones_potential#AB_form

They've effectively given you sqrt(A) and sqrt(B) rather than A and B directly.

-Justin


Could you please text some ideas, how could I use this? I want to check the
binding coordination of Zn with his amino acid residue in YodA (Zn binding
protein, 1oek.pdb), But after simulation (after 5 - 8ns), Zn-His bond was
dissociated.

or Could you type down some view on Zn-Nitrogen (Zn-Histidine) atom non
bonded parameter. I am using gromos96 53a6 ff.

I am new in this field so I would like to get some ideas about the same.

Thanks a lot



--
==

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] Regarding non-bonded parameter of Zn-His for gromos96 53a6 ff

[Navneet Chaturvedi]

Dear gmx user

I need help regarding changing the unit. I found a table in article (
http://pubs.acs.org/doi/abs/10.1021/jp501737x). There are some non bonded
parameters of metal ion given in *Ai* [kcal 1/2 mol −1/2 Å−6 ] and *Bi*
[kcal 1/2 mol −1/2 Å−3 ] unit. I want to use these values in c12 and c6
values (in case of amber ff sigma and epsilon).

Could you please text some ideas, how could I use this? I want to check the
binding coordination of Zn with his amino acid residue in YodA (Zn binding
protein, 1oek.pdb), But after simulation (after 5 - 8ns), Zn-His bond was
dissociated.

or Could you type down some view on Zn-Nitrogen (Zn-Histidine) atom non
bonded parameter. I am using gromos96 53a6 ff.

I am new in this field so I would like to get some ideas about the same.

Thanks a lot

-- 
*Your Sincerely*

*Dr Navaneet Chaturvedi*
C/O Dr Gali Prag
Department of Biochemistry & Mol Biology,
Sherman Building (The George S. Wise Faculty of Life Sciences)
Tel Aviv University, Tel Aviv 69978
Israel
Email: navaneet...@post.tau.ac.il
Skype: navneetonskype1
Web: http://www.praglab.org/#!members/cso6
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[gmx-users] Artificial Restraint/Wall/Potential at box top

[shivangi nangia]

Hello,

I have a system that contains 2000 CG POPC and 100 (21 AA) peptides.

I want to apply  a dummy wall at the top of the box so that my peptides do
not jump out of the box via PBC and re-enter the box from the bottom and
stick to the bilayer.

Is there a way to do that in GROMACS? distance restraint?


Kindly suggest.

Thanks in advance,
sxn
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[gmx-users] Position Restraints problem

[Chiara Bello]

Hi, I'm trying to apply the positions restraints only on alpha helices of my 
protein but after running mdrun, when I open the output pdb file using vmd, the 
protein appear broken: there are some atoms of the not restrained residues, 
that have been separated from the protein.
My simulation is in implicit solvent, I have used Charm27 and 
  
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[gmx-users] Do not consider the previous email, it was a mistake, I'm sorry.

[Chiara Bello]

From: kiarab...@msn.com
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Position Restraints problem
Date: Wed, 14 Oct 2015 13:07:41 +




Hi, I'm trying to apply the positions restraints only on alpha helices of my 
protein but after running mdrun, when I open the output pdb file using vmd, the 
protein appear broken: there are some atoms of the not restrained residues, 
that have been separated from the protein.
My simulation is in implicit solvent, I have used Charm27 and 

  
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