Re: [gmx-users] trjconv - two chains are separated

[Catarina A. Carvalheda dos Santos]

Hi there,

I had similar problems in the past. You'll have to play with trjconv and
find the best combination of different flags to solve the visualization
problem.

You can start by trying out this workflow for example:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Hope this helps.

Good luck!



On 3 February 2016 at 06:15, Trayder Thomas 
wrote:

> For "-pbc nojump" to work, you need to make sure they are together (as you
> want) in the first frame of your input trajectory.
>
> The most reliable way to do this is by centering the trajectory on a
> residue at the interface between the two chains (using a custom index
> group).
>
> I've also heard some people have had luck with "-pbc cluster"
>
> You can then run "-pbc nojump" on the centered (or clustered) trajectory.
>
> -Trayder
>
>
>
>
> On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu  wrote:
>
> > Hi Gromacs Users,
> >
> > I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my
> trajectories.
> > My protein has two chains (A and B) and they closely bind to each other.
> > after running trjconv with "-pbc nojump", two chains are greatly
> separated
> > by a certain distance. It is mostly likely that the pbc is not
> successfully
> > removed and the program takes a chain from one unit cell and another from
> > another unit cell.
> >
> > Does anybody have any idea to solve the problem?
> >
> > Best
> > Yunlong
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
-- 
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.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Yasser Almeida Hernández]

Hi Dries,

Let's say that the price is irrelevant right now. Just imagine an 
hardware with all the ideal features for the calculations.


Thanks all for your answers.

Best

Yasser


--

Hi Yasser,

Could you give us an idea of the price range you're looking at? I'd
probably try to get a laptop with a decent gpu to accelerate your work as
much as possible. Unfortunately, such laptops are often pricy.

Kind regards

Dries

On 3 February 2016 at 11:17, Yasser Almeida Hern?ndez <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:


Dear Joao,

I am aware that laptops are not the proper hardware to run MD simulations.
I do my runs in workstations designed for that purpose. The hardware I want
to buy is not just for simulations, but for general private/work purpose,
but I would like to have a device robust enough to run calculations. My
question was to get some thoughts about an ideal/optimal hardware.

Best

Yasser


Message: 6
Date: Wed, 3 Feb 2016 10:53:31 +0100
From: Jo?o Henriques 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Laptop features for MD simulations -
recommendations
Message-ID:
<
calc+hgt7zsmbkwitu11dprvh4m_qyw2btkgnsq2tvb70o71...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear Yasser,

I am by no means an expert on hardware, but I would strongly advise against
buying a laptop for the specific purpose of running (any and all) MD
simulations. A desktop is much better suited platform for such a task, as
you should be able to get a much bigger bang for your buck (this is the
main reason, but there are more cons).

Notice that I am not saying that you cannot run MD simulations on a laptop,
I'm just advising against it. In fact, you could probably run MD
simulations on a smartphone if you wanted to, but it doesn't sound like a
very good investment of your time and money. In my *personal opinion*, the
same holds true for the laptop.

Best regards,
/J

On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:

Hi all,


I want to buy a laptop suitable and powerful enough for MD simulations
with GROMACS (mostly membrane/protein systems). Could you recommend
optimal
features for this goal?

Thanks

Yasser

--
Yasser Almeida Hern?ndez
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c


--
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.

Re: [gmx-users] How the topology file is created based on *.gro file?

[Mark Abraham]

Hi,

Atom numbering is unimportant, but you might see warnings from tools that
recognise it is weird. Residue numbering is important only in that the
value changes when the residue does - it doesn't have to go up by one. Try
it and see ;-)

Mark

On Wed, 3 Feb 2016 10:13 Dawid das  wrote:

> Dear Gromacs Experts,
>
> Let's assume that I have a *.gro file in a proper format but the number of
> atoms and/or
> residues is let's say random, e.g. I have coordinates of atoms for residue
> 87, 95, 96, 88.
> What is more, I have let's say 76 atoms in the system, but I start
> numbering from 999.
> Will I be able to produce proper *.top file if the definition of atoms and
> their parameters
> is correct?
>
> Best wishes,
> Dawid Grabarek
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[João Henriques]

Dear Yasser,

I am by no means an expert on hardware, but I would strongly advise against
buying a laptop for the specific purpose of running (any and all) MD
simulations. A desktop is much better suited platform for such a task, as
you should be able to get a much bigger bang for your buck (this is the
main reason, but there are more cons).

Notice that I am not saying that you cannot run MD simulations on a laptop,
I'm just advising against it. In fact, you could probably run MD
simulations on a smartphone if you wanted to, but it doesn't sound like a
very good investment of your time and money. In my *personal opinion*, the
same holds true for the laptop.

Best regards,
/J

On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hernández <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:

> Hi all,
>
> I want to buy a laptop suitable and powerful enough for MD simulations
> with GROMACS (mostly membrane/protein systems). Could you recommend optimal
> features for this goal?
>
> Thanks
>
> Yasser
>
> --
> Yasser Almeida Hernández
> PhD student
> Institute of Biochemistry and Molecular Biology
> Department of Chemistry
> University of Hamburg
> Martin-Luther-King-Platz 6
> 20146 Hamburg
> Germany
> +49 40 42838 2845
> yasser.almeida.hernan...@chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Dries Van Rompaey]

Hi Yasser,

Could you give us an idea of the price range you're looking at? I'd
probably try to get a laptop with a decent gpu to accelerate your work as
much as possible. Unfortunately, such laptops are often pricy.

Kind regards

Dries

On 3 February 2016 at 11:17, Yasser Almeida Hernández <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:

> Dear Joao,
>
> I am aware that laptops are not the proper hardware to run MD simulations.
> I do my runs in workstations designed for that purpose. The hardware I want
> to buy is not just for simulations, but for general private/work purpose,
> but I would like to have a device robust enough to run calculations. My
> question was to get some thoughts about an ideal/optimal hardware.
>
> Best
>
> Yasser
>
> 
> Message: 6
> Date: Wed, 3 Feb 2016 10:53:31 +0100
> From: Jo?o Henriques 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Laptop features for MD simulations -
> recommendations
> Message-ID:
> <
> calc+hgt7zsmbkwitu11dprvh4m_qyw2btkgnsq2tvb70o71...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Yasser,
>
> I am by no means an expert on hardware, but I would strongly advise against
> buying a laptop for the specific purpose of running (any and all) MD
> simulations. A desktop is much better suited platform for such a task, as
> you should be able to get a much bigger bang for your buck (this is the
> main reason, but there are more cons).
>
> Notice that I am not saying that you cannot run MD simulations on a laptop,
> I'm just advising against it. In fact, you could probably run MD
> simulations on a smartphone if you wanted to, but it doesn't sound like a
> very good investment of your time and money. In my *personal opinion*, the
> same holds true for the laptop.
>
> Best regards,
> /J
>
> On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
>
> Hi all,
>>
>> I want to buy a laptop suitable and powerful enough for MD simulations
>> with GROMACS (mostly membrane/protein systems). Could you recommend
>> optimal
>> features for this goal?
>>
>> Thanks
>>
>> Yasser
>>
>> --
>> Yasser Almeida Hern?ndez
>> PhD student
>> Institute of Biochemistry and Molecular Biology
>> Department of Chemistry
>> University of Hamburg
>> Martin-Luther-King-Platz 6
>> 20146 Hamburg
>> Germany
>> +49 40 42838 2845
>> yasser.almeida.hernan...@chemie.uni-hamburg.de
>> office: Grindelallee 117, room 250c
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
> --
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 142, Issue 14
> **
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] How to visualizing gro file in pymol

[Dries Van Rompaey]

Hi,

Your tpr file only has information on the starting configuration (because
it's a file that stores everything you need to start your simulation, not a
file that contains your output). Your end point .gro file can be converted
into a pdb through editconf as well.

However, a better approach would be to visualise your trajectory (.trr or
.xtc) using trjconv (http://manual.gromacs.org/programs/gmx-trjconv.html).


Kind regards

Dries

On 3 February 2016 at 11:33, anu chandra  wrote:

> Hello all,
>
> I just finished a short simulation of a membrane protein system and trying
> to visualize the final gro file generated from the simulation using Pymol.
> Unfortunately, the Pymol failed to visualize the protein in cartoon
> representation. Though VMD can do the job, I just wonder is there a way I
> can visualize the gro file in Pymol. A quick surfing on web suggested to
> use the editconf to convert the .tpr file to .pdb file for visualizing with
> Pymol. Unfortunately, here the .tpr file have structural information from
> the beginning of the simulation rather than at the end of the simulation.
>
>
> Any suggestion would be very much appreciated.
>
>
> Many thanks
> Anu
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Modified peptides

[Justin Lemkul]

On 2/2/16 11:02 AM, sun wrote:

Hello
I want to do protein-ligand MD with Gromos-43A1 ff. My ligand is a tripeptide 
with a heterocyclic ring  attached to -N terminus. I read in Justin's tutorial, 
for non-peptidic ligands, one can obtain co-ordinates from PRODRG server. My 
question is, if i can obtain the co-ordinates for modified peptide as well? 
Will it behave like a peptide then? Or should i define the paramenters for 
ring,alone, from PRODRG, run pdb2gmx for peptide lligand and then combine the 
co-ordinates into a file and then prepare topology for my protein and make 
complex.gro?



You should not use PRODRG for anything; its parameters are quite unreliable.

Use the protein force field for anything with protein and develop parameters for 
the rest.  This will involve parametrizing a suitable model compound that 
contains the linkage to the peptide, so that the topology can be merged easily 
to create a new residue or terminus definition.


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] How to visualizing gro file in pymol

[Diogo Vila Viçosa]

This can help you:

http://manual.gromacs.org/programs/gmx-editconf.html

Nevertheless, you can simply type: editconf -f structure.gro -o
structure.pdb


On Wed, Feb 3, 2016 at 10:34 AM anu chandra  wrote:

> Hello all,
>
> I just finished a short simulation of a membrane protein system and trying
> to visualize the final gro file generated from the simulation using Pymol.
> Unfortunately, the Pymol failed to visualize the protein in cartoon
> representation. Though VMD can do the job, I just wonder is there a way I
> can visualize the gro file in Pymol. A quick surfing on web suggested to
> use the editconf to convert the .tpr file to .pdb file for visualizing with
> Pymol. Unfortunately, here the .tpr file have structural information from
> the beginning of the simulation rather than at the end of the simulation.
>
>
> Any suggestion would be very much appreciated.
>
>
> Many thanks
> Anu
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] How the topology file is created based on *.gro file?

[Diogo Vila Viçosa]

If you still need to correct your numbering (for scripting porposes for
example) you can convert your original.gro using editconf and in the final
gro file will be corrected.

On Wed, Feb 3, 2016 at 11:24 AM Dawid das  wrote:

> So it turns out that what is important is the order, i.e. when I want
> connection
> between residues 164 and 165 they need to go in order in my *gro file.
> Otherwise there
> won't be any bonding in the topology.
>
> Best wishes,
> Dawid Grabarek
>
> 2016-02-03 10:29 GMT+01:00 Mark Abraham :
>
> > Hi,
> >
> > Atom numbering is unimportant, but you might see warnings from tools that
> > recognise it is weird. Residue numbering is important only in that the
> > value changes when the residue does - it doesn't have to go up by one.
> Try
> > it and see ;-)
> >
> > Mark
> >
> > On Wed, 3 Feb 2016 10:13 Dawid das  wrote:
> >
> > > Dear Gromacs Experts,
> > >
> > > Let's assume that I have a *.gro file in a proper format but the number
> > of
> > > atoms and/or
> > > residues is let's say random, e.g. I have coordinates of atoms for
> > residue
> > > 87, 95, 96, 88.
> > > What is more, I have let's say 76 atoms in the system, but I start
> > > numbering from 999.
> > > Will I be able to produce proper *.top file if the definition of atoms
> > and
> > > their parameters
> > > is correct?
> > >
> > > Best wishes,
> > > Dawid Grabarek
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Laptop features for MD simulations - recommendations

[Yasser Almeida Hernández]

Hi all,

I want to buy a laptop suitable and powerful enough for MD simulations 
with GROMACS (mostly membrane/protein systems). Could you recommend 
optimal features for this goal?


Thanks

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

--
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.

[gmx-users] Thermal energy

[gozde ergin]

Dear users,

Is there way to extract the thermal energy of the system that simulated in
NVT ensemble?

thanks
-- 
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.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Yasser Almeida Hernández]

Dear Joao,

I am aware that laptops are not the proper hardware to run MD 
simulations. I do my runs in workstations designed for that purpose. The 
hardware I want to buy is not just for simulations, but for general 
private/work purpose, but I would like to have a device robust enough to 
run calculations. My question was to get some thoughts about an 
ideal/optimal hardware.


Best

Yasser


Message: 6
Date: Wed, 3 Feb 2016 10:53:31 +0100
From: Jo?o Henriques 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Laptop features for MD simulations -
recommendations
Message-ID:

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

Dear Yasser,

I am by no means an expert on hardware, but I would strongly advise against
buying a laptop for the specific purpose of running (any and all) MD
simulations. A desktop is much better suited platform for such a task, as
you should be able to get a much bigger bang for your buck (this is the
main reason, but there are more cons).

Notice that I am not saying that you cannot run MD simulations on a laptop,
I'm just advising against it. In fact, you could probably run MD
simulations on a smartphone if you wanted to, but it doesn't sound like a
very good investment of your time and money. In my *personal opinion*, the
same holds true for the laptop.

Best regards,
/J

On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:


Hi all,

I want to buy a laptop suitable and powerful enough for MD simulations
with GROMACS (mostly membrane/protein systems). Could you recommend optimal
features for this goal?

Thanks

Yasser

--
Yasser Almeida Hern?ndez
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

End of gromacs.org_gmx-users Digest, Vol 142, Issue 14
**



--
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.

[gmx-users] How to visualizing gro file in pymol

[anu chandra]

Hello all,

I just finished a short simulation of a membrane protein system and trying
to visualize the final gro file generated from the simulation using Pymol.
Unfortunately, the Pymol failed to visualize the protein in cartoon
representation. Though VMD can do the job, I just wonder is there a way I
can visualize the gro file in Pymol. A quick surfing on web suggested to
use the editconf to convert the .tpr file to .pdb file for visualizing with
Pymol. Unfortunately, here the .tpr file have structural information from
the beginning of the simulation rather than at the end of the simulation.


Any suggestion would be very much appreciated.


Many thanks
Anu
-- 
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.

Re: [gmx-users] dna topology in OPLS force field

[Justin Lemkul]

On 2/2/16 11:53 AM, soumadwip ghosh wrote:

Hello,
 I am facing some difficulty to simulate single stranded DNA and a
single walled acrbon nanotube. I need different CNTs (with various m and n)
for my study and I am generating them using g_x2top accoring to Andrea
Mineoi's tutorial. It seems to be ok. On the other hand I have to make
topology for ssDNA which I am finding very difficult to generate using OPLS
force field. I tried Topolgen and Topolbuilder both but in the output
topology atomtypes are not defined and the net charge comes out to be zero
which should be -11. My question is is there a possible way to generate
CNTs in combination with CHARMM27 force field with pdb2gmx with all the
dihedral and angle parameters unambiguously. I guess I cannot use g_x2top
in connection with CHARMM. Or is there a way to convert the cnt.top I have


That's not correct; you can use x2top with any force field, you just have to 
write a .n2t file.



(the OPLS one) into CHARMM atomtypes and parameters? I would appreciate any
insight in this regard. Sorry for asking much.



In principle, a CNT is just the same atom type over and over again (unless 
you've got capping groups on the end) and a few bonded parameters.  It should be 
very simple to write a topology.  Whether or not this representation is adequate 
to describe the physics is another matter.


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gromos43a1p-4.5.1.tgz can alos used for TPO and SEP

[Justin Lemkul]

On 2/3/16 2:40 AM, Mehreen Jan wrote:

repected sir !
i also used the following forefield but it did not work. same error residue TPO 
is not found in residues topology database

gromos43a1p-4.5.1.tgz
Force field files for Gromos96 43a1p, re-formatted to be compatible with newer 
versions of Gromacs (4.0 and beyond). This particular archive organizes the 
files such that they are compatible with version 4.5.x. Please note that the 
parameters are unmodified relative to what was contributed by Graham Smith. I 
take no credit for these parameters; I just made the files compatible with the 
current version of Gromacs. This version includes files that were missing in 
the previous tarball.



The force field works.  You're probably just picking the wrong one from the list 
provided by pdb2gmx.  Remember that if you're adding a new force field it must 
either be in $GMXLIB or the working directory.


If you are still unable to make this work, please provide (copy and paste) the 
full screen output from pdb2gmx, including your command line and all your 
selections (not just the error message).


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] How the topology file is created based on *.gro file?

[Dawid das]

So it turns out that what is important is the order, i.e. when I want
connection
between residues 164 and 165 they need to go in order in my *gro file.
Otherwise there
won't be any bonding in the topology.

Best wishes,
Dawid Grabarek

2016-02-03 10:29 GMT+01:00 Mark Abraham :

> Hi,
>
> Atom numbering is unimportant, but you might see warnings from tools that
> recognise it is weird. Residue numbering is important only in that the
> value changes when the residue does - it doesn't have to go up by one. Try
> it and see ;-)
>
> Mark
>
> On Wed, 3 Feb 2016 10:13 Dawid das  wrote:
>
> > Dear Gromacs Experts,
> >
> > Let's assume that I have a *.gro file in a proper format but the number
> of
> > atoms and/or
> > residues is let's say random, e.g. I have coordinates of atoms for
> residue
> > 87, 95, 96, 88.
> > What is more, I have let's say 76 atoms in the system, but I start
> > numbering from 999.
> > Will I be able to produce proper *.top file if the definition of atoms
> and
> > their parameters
> > is correct?
> >
> > Best wishes,
> > Dawid Grabarek
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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.

[gmx-users] How the topology file is created based on *.gro file?

[Dawid das]

Dear Gromacs Experts,

Let's assume that I have a *.gro file in a proper format but the number of
atoms and/or
residues is let's say random, e.g. I have coordinates of atoms for residue
87, 95, 96, 88.
What is more, I have let's say 76 atoms in the system, but I start
numbering from 999.
Will I be able to produce proper *.top file if the definition of atoms and
their parameters
is correct?

Best wishes,
Dawid Grabarek
-- 
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.

[gmx-users] GROMACS 5.1.2 official release

[Mark Abraham]

Hi GROMACS users,

The official release of GROMACS 5.1.2 is available!

This release fixes some known issues in 5.1.1. We encourage all users of
the 5.1 series to update to 5.1.2. Please see the link to the release notes
below for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.2.tar.gz
http://manual.gromacs.org/documentation/5.1.2/index.html (including
installation guide, user guide, reference manual)
http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/index.html
http://gerrit.gromacs.org/download/regressiontests-5.1.2.tar.gz

Happy simulating!

Mark Abraham
GROMACS development manager
-- 
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.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Mark Abraham]

Hi,

I'd be thinking in terms of a 4-core Haswell processor and a GTX 980. If
you want to run GROMACS then you can't skimp on the CPU, but the more cores
it has, the lower the battery life when you're just doing routine
non-computational things, because many laptop computing needs don't
actually use more than one core. For example, my 2014-model Macbook Air has
a 2-core Haswell that has beautiful battery life until you actually start
hitting the processor (usually for GROMACS compilation, in my case). So
maybe 2-core Haswell and a GTX 780 gives a better all-round machine.

Mark

On Wed, Feb 3, 2016 at 1:25 PM João Henriques <
joao.henriques.32...@gmail.com> wrote:

> Well, in that case Dries has already answered your question.
>
> In sum, any laptop will do as long as it is equipped with a decent GPU. The
> GPU is probably more important than the CPU and RAM. There are several
> benchmarks by NVIDIA for GPU performance with Gromacs. If you ask them,
> they'll probably try to "sell" you their high-end products, but there's
> been several demonstrations that cheaper GPUs perform almost as well. For
> example, I clearly remember Erik Lindahl at one of those NVIDIA online
> presentations showing that an inexpensive GTX did almost as well as a much
> more expensive K20. NVIDIA's host probably wasn't very pleased with it.
>
> Moreover, even if money is not an issue, power supply and actual space to
> fit the parts are big problems on a laptop. I mean, don't expect to be able
> to fit and feed two 10-core Intel E5-2650v3 2.3 GHz CPUs, 64 Gb RAM, 2 TB
> disk and two NVIDIA K80's on a 13 inch notebook case :)
>
> Best regards,
> João
>
>
>
> On Wed, Feb 3, 2016 at 11:56 AM, Yasser Almeida Hernández <
> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
>
> > Hi Dries,
> >
> > Let's say that the price is irrelevant right now. Just imagine an
> hardware
> > with all the ideal features for the calculations.
> >
> > Thanks all for your answers.
> >
> > Best
> >
> > Yasser
> >
> >
> > --
> >
> > Hi Yasser,
> >
> > Could you give us an idea of the price range you're looking at? I'd
> > probably try to get a laptop with a decent gpu to accelerate your work as
> > much as possible. Unfortunately, such laptops are often pricy.
> >
> > Kind regards
> >
> > Dries
> >
> > On 3 February 2016 at 11:17, Yasser Almeida Hern?ndez <
> >
> > yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
> >
> > Dear Joao,
> >>
> >> I am aware that laptops are not the proper hardware to run MD
> simulations.
> >> I do my runs in workstations designed for that purpose. The hardware I
> >> want
> >> to buy is not just for simulations, but for general private/work
> purpose,
> >> but I would like to have a device robust enough to run calculations. My
> >> question was to get some thoughts about an ideal/optimal hardware.
> >>
> >> Best
> >>
> >> Yasser
> >>
> >> 
> >> Message: 6
> >> Date: Wed, 3 Feb 2016 10:53:31 +0100
> >> From: Jo?o Henriques 
> >> To: Discussion list for GROMACS users 
> >> Subject: Re: [gmx-users] Laptop features for MD simulations -
> >> recommendations
> >> Message-ID:
> >> <
> >> calc+hgt7zsmbkwitu11dprvh4m_qyw2btkgnsq2tvb70o71...@mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> Dear Yasser,
> >>
> >> I am by no means an expert on hardware, but I would strongly advise
> >> against
> >> buying a laptop for the specific purpose of running (any and all) MD
> >> simulations. A desktop is much better suited platform for such a task,
> as
> >> you should be able to get a much bigger bang for your buck (this is the
> >> main reason, but there are more cons).
> >>
> >> Notice that I am not saying that you cannot run MD simulations on a
> >> laptop,
> >> I'm just advising against it. In fact, you could probably run MD
> >> simulations on a smartphone if you wanted to, but it doesn't sound like
> a
> >> very good investment of your time and money. In my *personal opinion*,
> the
> >> same holds true for the laptop.
> >>
> >> Best regards,
> >> /J
> >>
> >> On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
> >> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
> >>
> >> Hi all,
> >>
> >>>
> >>> I want to buy a laptop suitable and powerful enough for MD simulations
> >>> with GROMACS (mostly membrane/protein systems). Could you recommend
> >>> optimal
> >>> features for this goal?
> >>>
> >>> Thanks
> >>>
> >>> Yasser
> >>>
> >>> --
> >>> Yasser Almeida Hern?ndez
> >>> PhD student
> >>> Institute of Biochemistry and Molecular Biology
> >>> Department of Chemistry
> >>> University of Hamburg
> >>> Martin-Luther-King-Platz 6
> >>> 20146 Hamburg
> >>> Germany
> >>> +49 40 42838 2845
> >>> yasser.almeida.hernan...@chemie.uni-hamburg.de
> >>> office: Grindelallee 117, room 250c
> >>>
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > 

Re: [gmx-users] trjconv options?

[Justin Lemkul]

On 2/3/16 6:34 AM, Timofey Tyugashev wrote:

Thank you for replies on my previous questions.
And now I have another one dealing with trjconv.

I have a simulation of  a three-chain protein/nucleic acid complex. Naturally,
it gets broken in three separate strands by PBC.
After trying several, I settled on using options '-pbc mol' with '-ur compact'
which makes the complex look decent again and it looks like that does the job.
But I'm worried about a possibility of something getting unrepaired by this
option and getting unnoticed by me. What is the way to check for it?


Any molecules that appear to fly away suddenly will be a pretty dead giveaway.

In general, for multimeric complexes, you need to do a lot more work, e.g. 
centering on a single chain after making molecules whole and removing jumps.  If 
a simple -pbc mol -ur compact does the trick, probably nothing has actually 
crossed a periodic boundary yet.



Also it keeps tumbling around the cell during the trajectory. It's annoying. Is
there a way to pin down the cluster and stop it from rotating?


This is what trjconv -fit 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

==
--
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.

Re: [gmx-users] How to visualizing gro file in pymol

[Catarina A. Carvalheda dos Santos]

Hi Anu,

You can always use ediconf to convert your .gro file into a .pdb file =)

For multiple chain systems Pymol needs the chain information in the
structure file. Because .gro files don't have the chain info, you'll always
need a .pdb file.
If this is your case, that's the reason why the cartoon representation
isn't working.

Hope this helps,

Cheers,

On 3 February 2016 at 10:33, anu chandra  wrote:

> Hello all,
>
> I just finished a short simulation of a membrane protein system and trying
> to visualize the final gro file generated from the simulation using Pymol.
> Unfortunately, the Pymol failed to visualize the protein in cartoon
> representation. Though VMD can do the job, I just wonder is there a way I
> can visualize the gro file in Pymol. A quick surfing on web suggested to
> use the editconf to convert the .tpr file to .pdb file for visualizing with
> Pymol. Unfortunately, here the .tpr file have structural information from
> the beginning of the simulation rather than at the end of the simulation.
>
>
> Any suggestion would be very much appreciated.
>
>
> Many thanks
> Anu
> --
> 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.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
-- 
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.

[gmx-users] trjconv options?

[Timofey Tyugashev]

Thank you for replies on my previous questions.
And now I have another one dealing with trjconv.

I have a simulation of  a three-chain protein/nucleic acid complex. 
Naturally, it gets broken in three separate strands by PBC.
After trying several, I settled on using options '-pbc mol' with '-ur 
compact' which makes the complex look decent again and it looks like 
that does the job.
But I'm worried about a possibility of something getting unrepaired by 
this option and getting unnoticed by me. What is the way to check for it?
Also it keeps tumbling around the cell during the trajectory. It's 
annoying. Is there a way to pin down the cluster and stop it from rotating?

--
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.

Re: [gmx-users] How the topology file is created based on *.gro file?

[Dawid das]

Okay, now when I did some tests I can explain more precisely what I want to
do.

As I wrote in my other message, I have to cut out some of the amino acids
from my protein.
They are supposed to create an environment around the central amino acid
residue (chromophore in my case).
Because the peptide bonds were cleaved I want to cap them with methyl
groups. I start from *.gro file
with results from MD trajectory.

So I cut out the environment, let's say residues 34, 55-56-57 and 89 from
my original *.gro file
and create new cut-out.gro file. Now I need those methyl groups to cap both
ends of residues 34 and 89
, the N-end of residue 55 and C-end of residue 57. So the order of residues
in my cut-out.gro file
must be like:
100
34
101
102
55
56
57
103
104
89
105

I used 100-105 for methyl "residues" (I guess I will manage to define them
as I have already done this kind
of stuff) numbering because this number does not matter. It's just an
example.
So now my question is won't pdb2gmx create bonds between 101 -  102
residues or 103-104?
I don't want that obviously.

And one more thing. Is it possible to create proper bonds when the order of
my residues is like:
34
55
56
57
89
100
101
.
.
.

so no bond between 34 - 55 but bonds between 100 - 34 - 101 , 102 - 55 and
so on?

Best wishes,
Dawid Grabarek

2016-02-03 12:29 GMT+01:00 Diogo Vila Viçosa :

> If you still need to correct your numbering (for scripting porposes for
> example) you can convert your original.gro using editconf and in the final
> gro file will be corrected.
>
> On Wed, Feb 3, 2016 at 11:24 AM Dawid das  wrote:
>
> > So it turns out that what is important is the order, i.e. when I want
> > connection
> > between residues 164 and 165 they need to go in order in my *gro file.
> > Otherwise there
> > won't be any bonding in the topology.
> >
> > Best wishes,
> > Dawid Grabarek
> >
> > 2016-02-03 10:29 GMT+01:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > Atom numbering is unimportant, but you might see warnings from tools
> that
> > > recognise it is weird. Residue numbering is important only in that the
> > > value changes when the residue does - it doesn't have to go up by one.
> > Try
> > > it and see ;-)
> > >
> > > Mark
> > >
> > > On Wed, 3 Feb 2016 10:13 Dawid das  wrote:
> > >
> > > > Dear Gromacs Experts,
> > > >
> > > > Let's assume that I have a *.gro file in a proper format but the
> number
> > > of
> > > > atoms and/or
> > > > residues is let's say random, e.g. I have coordinates of atoms for
> > > residue
> > > > 87, 95, 96, 88.
> > > > What is more, I have let's say 76 atoms in the system, but I start
> > > > numbering from 999.
> > > > Will I be able to produce proper *.top file if the definition of
> atoms
> > > and
> > > > their parameters
> > > > is correct?
> > > >
> > > > Best wishes,
> > > > Dawid Grabarek
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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.

Re: [gmx-users] How the topology file is created based on *.gro file?

[Mark Abraham]

Hi,

These things can all be handled by pdb2gmx chain-separation (which
regulates whether the topology generator will expect to make bonds between
residues adjacent in the sequence in the input file) and merging machinery
(if you want your cutout region to be all in the same [moleculetype] or
not), based on either PDB chain ID, TER records or both. See gmx pdb2gmx -h.

Mark

On Wed, Feb 3, 2016 at 12:42 PM Dawid das  wrote:

> Okay, now when I did some tests I can explain more precisely what I want to
> do.
>
> As I wrote in my other message, I have to cut out some of the amino acids
> from my protein.
> They are supposed to create an environment around the central amino acid
> residue (chromophore in my case).
> Because the peptide bonds were cleaved I want to cap them with methyl
> groups. I start from *.gro file
> with results from MD trajectory.
>
> So I cut out the environment, let's say residues 34, 55-56-57 and 89 from
> my original *.gro file
> and create new cut-out.gro file. Now I need those methyl groups to cap both
> ends of residues 34 and 89
> , the N-end of residue 55 and C-end of residue 57. So the order of residues
> in my cut-out.gro file
> must be like:
> 100
> 34
> 101
> 102
> 55
> 56
> 57
> 103
> 104
> 89
> 105
>
> I used 100-105 for methyl "residues" (I guess I will manage to define them
> as I have already done this kind
> of stuff) numbering because this number does not matter. It's just an
> example.
> So now my question is won't pdb2gmx create bonds between 101 -  102
> residues or 103-104?
> I don't want that obviously.
>
> And one more thing. Is it possible to create proper bonds when the order of
> my residues is like:
> 34
> 55
> 56
> 57
> 89
> 100
> 101
> .
> .
> .
>
> so no bond between 34 - 55 but bonds between 100 - 34 - 101 , 102 - 55 and
> so on?
>
> Best wishes,
> Dawid Grabarek
>
> 2016-02-03 12:29 GMT+01:00 Diogo Vila Viçosa :
>
> > If you still need to correct your numbering (for scripting porposes for
> > example) you can convert your original.gro using editconf and in the
> final
> > gro file will be corrected.
> >
> > On Wed, Feb 3, 2016 at 11:24 AM Dawid das  wrote:
> >
> > > So it turns out that what is important is the order, i.e. when I want
> > > connection
> > > between residues 164 and 165 they need to go in order in my *gro file.
> > > Otherwise there
> > > won't be any bonding in the topology.
> > >
> > > Best wishes,
> > > Dawid Grabarek
> > >
> > > 2016-02-03 10:29 GMT+01:00 Mark Abraham :
> > >
> > > > Hi,
> > > >
> > > > Atom numbering is unimportant, but you might see warnings from tools
> > that
> > > > recognise it is weird. Residue numbering is important only in that
> the
> > > > value changes when the residue does - it doesn't have to go up by
> one.
> > > Try
> > > > it and see ;-)
> > > >
> > > > Mark
> > > >
> > > > On Wed, 3 Feb 2016 10:13 Dawid das  wrote:
> > > >
> > > > > Dear Gromacs Experts,
> > > > >
> > > > > Let's assume that I have a *.gro file in a proper format but the
> > number
> > > > of
> > > > > atoms and/or
> > > > > residues is let's say random, e.g. I have coordinates of atoms for
> > > > residue
> > > > > 87, 95, 96, 88.
> > > > > What is more, I have let's say 76 atoms in the system, but I start
> > > > > numbering from 999.
> > > > > Will I be able to produce proper *.top file if the definition of
> > atoms
> > > > and
> > > > > their parameters
> > > > > is correct?
> > > > >
> > > > > Best wishes,
> > > > > Dawid Grabarek
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > 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 

Re: [gmx-users] Laptop features for MD simulations - recommendations

[João Henriques]

Well, in that case Dries has already answered your question.

In sum, any laptop will do as long as it is equipped with a decent GPU. The
GPU is probably more important than the CPU and RAM. There are several
benchmarks by NVIDIA for GPU performance with Gromacs. If you ask them,
they'll probably try to "sell" you their high-end products, but there's
been several demonstrations that cheaper GPUs perform almost as well. For
example, I clearly remember Erik Lindahl at one of those NVIDIA online
presentations showing that an inexpensive GTX did almost as well as a much
more expensive K20. NVIDIA's host probably wasn't very pleased with it.

Moreover, even if money is not an issue, power supply and actual space to
fit the parts are big problems on a laptop. I mean, don't expect to be able
to fit and feed two 10-core Intel E5-2650v3 2.3 GHz CPUs, 64 Gb RAM, 2 TB
disk and two NVIDIA K80's on a 13 inch notebook case :)

Best regards,
João



On Wed, Feb 3, 2016 at 11:56 AM, Yasser Almeida Hernández <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:

> Hi Dries,
>
> Let's say that the price is irrelevant right now. Just imagine an hardware
> with all the ideal features for the calculations.
>
> Thanks all for your answers.
>
> Best
>
> Yasser
>
>
> --
>
> Hi Yasser,
>
> Could you give us an idea of the price range you're looking at? I'd
> probably try to get a laptop with a decent gpu to accelerate your work as
> much as possible. Unfortunately, such laptops are often pricy.
>
> Kind regards
>
> Dries
>
> On 3 February 2016 at 11:17, Yasser Almeida Hern?ndez <
>
> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
>
> Dear Joao,
>>
>> I am aware that laptops are not the proper hardware to run MD simulations.
>> I do my runs in workstations designed for that purpose. The hardware I
>> want
>> to buy is not just for simulations, but for general private/work purpose,
>> but I would like to have a device robust enough to run calculations. My
>> question was to get some thoughts about an ideal/optimal hardware.
>>
>> Best
>>
>> Yasser
>>
>> 
>> Message: 6
>> Date: Wed, 3 Feb 2016 10:53:31 +0100
>> From: Jo?o Henriques 
>> To: Discussion list for GROMACS users 
>> Subject: Re: [gmx-users] Laptop features for MD simulations -
>> recommendations
>> Message-ID:
>> <
>> calc+hgt7zsmbkwitu11dprvh4m_qyw2btkgnsq2tvb70o71...@mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Yasser,
>>
>> I am by no means an expert on hardware, but I would strongly advise
>> against
>> buying a laptop for the specific purpose of running (any and all) MD
>> simulations. A desktop is much better suited platform for such a task, as
>> you should be able to get a much bigger bang for your buck (this is the
>> main reason, but there are more cons).
>>
>> Notice that I am not saying that you cannot run MD simulations on a
>> laptop,
>> I'm just advising against it. In fact, you could probably run MD
>> simulations on a smartphone if you wanted to, but it doesn't sound like a
>> very good investment of your time and money. In my *personal opinion*, the
>> same holds true for the laptop.
>>
>> Best regards,
>> /J
>>
>> On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
>> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
>>
>> Hi all,
>>
>>>
>>> I want to buy a laptop suitable and powerful enough for MD simulations
>>> with GROMACS (mostly membrane/protein systems). Could you recommend
>>> optimal
>>> features for this goal?
>>>
>>> Thanks
>>>
>>> Yasser
>>>
>>> --
>>> Yasser Almeida Hern?ndez
>>> PhD student
>>> Institute of Biochemistry and Molecular Biology
>>> Department of Chemistry
>>> University of Hamburg
>>> Martin-Luther-King-Platz 6
>>> 20146 Hamburg
>>> Germany
>>> +49 40 42838 2845
>>> yasser.almeida.hernan...@chemie.uni-hamburg.de
>>> office: Grindelallee 117, room 250c
>>>
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Nstlist and constrain simulations

[Mark Abraham]

Hi,

Agree, if it is drift related, then the real problem should be so bad that
pretty much any observable should show junk!

Mark

On Wed, 3 Feb 2016 22:50 Szilárd Páll  wrote:

> --
> Szilárd
>
>
> On Tue, Feb 2, 2016 at 4:23 PM, Mark Abraham 
> wrote:
> > Hi,
> >
> > On Tue, Feb 2, 2016 at 1:11 PM Michail Palaiokostas Avramidis <
> > m.palaiokos...@qmul.ac.uk> wrote:
> >
> >> Hi Mark and thank you for your answer.
> >> Please see below :)
> >>
> >> On 01/02/16 18:28, Mark Abraham wrote:
> >> > Hi,
> >> >
> >> > On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis <
> >> > m.palaiokos...@qmul.ac.uk> wrote:
> >> >
> >> >> Dear GMX users,
> >> >>
> >> >>
> >> >> I would like to ask about your opinion on the size of the neighbour
> list
> >> >> (nstlist).
> >> >>
> >> >>
> >> >> I am running constraint simulations
> >> >
> >> > What do you mean by a "constraint simulation?"
> >> Sorry, I should have been clearer. I am using the z-constraint method in
> >> which I constrain the permeant along the z-axis in various positions and
> >> I record the constraint force. Similar to umbrella sampling but with
> >> constrained distances between the permeant and membrane.
> >>
> >
> > Using which GROMACS feature? e.g. freeze groups and NPT are usually an
> > unhappy combination.
> >
> >
> >> >> of a permeant along a lipid bilayer. In the initial setup the system
> >> runs
> >> >> on NPT and nstlist 10 (which GROMACS changes to 40 automatically).
> With
> >> >> this setup my simulation is very fast but always crashes at various
> >> points
> >> >> with the same way always. Initially it gives some LINCS warnings and
> >> then
> >> >> it gives an error that a particle "communicated to PME rank 2 are
> more
> >> than
> >> >> 2/3 times the cut-off out of the domain decomposition cell".
> >> >>
> >> > Usually this indicates your setup is unstable e.g. see
> >> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up. I'll
> >> proceed
> >> > by assuming you're very confident that your membrane system has had a
> >> > suitable few dozen+ nanoseconds of equilibration ;-)
> >> Yes absolutely confident. The system does not crash with unconstrained
> >> simulations. The membrane-solvent system is well equilibrated for 1μs
> >> and then, after I introduce the permeant, I perform an energy
> >> minimization and a short 500ps NPT-Berendsen equilibration to relax the
> >> pressure that the permeant might have introduced.
> >>
> >
> > I'd be skeptical that 500ps was enough.
> >
> >
> >> > When I see the last pdb steps before crash, sometimes there seem to be
> >> >> overlaps between the permeants and the lipids and then system
> explosions
> >> >> and PBChaos. Other times it is not so dramatic.
> >> >>
> >> >>
> >> >> So the question is, should I be conservative with the nstlist? When I
> >> run
> >> >> NPT simulations and change the nstlist to 1, the system does not
> fail.
> >> >> Alternatively, if I change to NVT and nstlist to 10, again the system
> >> runs
> >> >> successfully. But NVT and 40 crashes.
> >> >>
> >> > This might all be a wild goose chase. If you are pulling permeants
> into
> >> the
> >> > membrane, then that creates pressure on the membrane and perhaps
> >> > destabilizes the pressure coupling. If that's with Parrinello-Rahman
> then
> >> > it can easily oscillate out of control, ending up violating the
> >> assumptions
> >> > under which the code is written.
> >> Yes, this is why I run an small equilibration in the beginning. And to
> >> be honest, technically, I do not pull the permeants. For each position,
> >> I add it to the system in VMD, and then run the
> >> minimization-equilibration-production sequence.
> >> >
> >> > Since GROMACS was doing the nstlist update automatically, I thought it
> >> was
> >> >> a "safe" option. Based on the above,however, I believe that since the
> >> >> simulation runs with constraints, the system is more sensitive and
> thus
> >> the
> >> >> nstlist should be smaller. Can anyone validate that my hypothesis is
> >> >> correct?
> >> >>
> >> > On the limited evidence available, I think your observations are more
> >> > likely to be symptoms of the problem than the problem itself. How does
> >> e.g.
> >> > one permeant molecule behave?
> >> Once again sorry for not being clear. The plural in permeants comes from
> >> the fact that I test several molecules (e.g. water, ammonia etc) but it
> >> is only one per simulation/system.
> >>
> >> So, you think that the updating of neighbour list, shouldn't affect the
> >> problem?
> >>
> >
> > Yep. You can force mdrun to use an nstlist of your choosing with mdrun
> > -nstlist n. I would expect you to observe similar instability in such
> > cases. The only case in which I think nstlist could matter is when
> > something else is so badly wrong that particles diffuse further than the
> > automated buffer anticipates, in which case any reduction of nstlist that
> > keeps the 

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Davide Cruz]

Hi,

Well if you already have a laptop with a decent cpu you could consider an
external gpu. There are companies that sell that kind of hardware
solutions, but, they are expensive. On the other hand, if you have a DIYer
vein, you could build an eGPU solution. This would require a desktop gpu
and power supply, and the connector with the pci express interface. There
are some tutorials on the web.
Of course this would kill mobility, but the bang for the buck when compared
to a enthusiast level laptop would be higher. Moreover, this kind of system
is less prone to overheat, as the gpu's tend to run hot, and cramming
powerhouses in tiny cases doesn't help cooling at all.

Cheers

Davide Cruz
On 3 Feb 2016 8:25 p.m., "Szilárd Páll"  wrote:

> On Wed, Feb 3, 2016 at 8:46 PM, Dries Van Rompaey
>  wrote:
> > Hi,
> >
> > Just to expand a bit on Szilárd’s excellent answer, you can find a list
> of benchmarks for mobile cards here:
> >
> http://www.notebookcheck.net/Mobile-Graphics-Cards-Benchmark-List.844.0.html
>
> Note: even though you see quite high on that list GTX 7xx series GPUs,
> I strongly suggest to go with 9xx instead. Given the perf/W increase
> Kepler to Maxwell (for measured values see our recent paper on GROMACS
> hardware benchmarking), putting everything but performance aside, with
> the amount of heat that can be extracted from the laptop enclosure
> you'll get a lot more performance with the latter.
> Same goes for AMD, the cards are decent with our OpenCL support, but
> can only about match the Kepler-gen cards.
>
> > Kind regards
> >
> > Dries
> >
> >
> >> On 03 Feb 2016, at 15:14, Szilárd Páll  wrote:
> >>
> >> Hi,
> >>
> >> What exactly do you want from the laptop besides performance?
> >> Autonomy, weight, size restrictions?
> >>
> >> If you want something with a decent amount of autonomy, just get a
> >> high-end Skylake laptop and do your runs on your workstation or
> >> cluster. If you care about battery time, you may as well forget about
> >> a powerful system (even a standalone GPU may not be worth it unless
> >> you can get switchable graphics) - or at least plan to put effort into
> >> avoiding high CPU/GPU load when on battery.
> >>
> >> If you want max performance, get a beast that's often referred to as
> >> "portable workstation" with a high-performance CPU (not 15W part) and
> >> a GTX 970M or 980M. AFAIK NVIDIAs site has a section where they
> >> advertise gaming laptops with these high-end mobile chips.
> >>
> >> Unless you want to suffer with Windows, I'd also recommend looking
> >> around before buying and making sure that you don't end up with some
> >> niche hardware that does not run well under GNU/Linux. I can highly
> >> recommend System76, they have some monsters too - I have even seen
> >> recently a rave review about a portable workstation they offer with a
> >> desktop CPU.
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >>
> >>
> >> On Wed, Feb 3, 2016 at 11:17 AM, Yasser Almeida Hernández
> >>  wrote:
> >>> Dear Joao,
> >>>
> >>> I am aware that laptops are not the proper hardware to run MD
> simulations. I
> >>> do my runs in workstations designed for that purpose. The hardware I
> want to
> >>> buy is not just for simulations, but for general private/work purpose,
> but I
> >>> would like to have a device robust enough to run calculations. My
> question
> >>> was to get some thoughts about an ideal/optimal hardware.
> >>>
> >>> Best
> >>>
> >>> Yasser
> >>>
> >>> 
> >>> Message: 6
> >>> Date: Wed, 3 Feb 2016 10:53:31 +0100
> >>> From: Jo?o Henriques 
> >>> To: Discussion list for GROMACS users 
> >>> Subject: Re: [gmx-users] Laptop features for MD simulations -
> >>>recommendations
> >>> Message-ID:
> >>><
> calc+hgt7zsmbkwitu11dprvh4m_qyw2btkgnsq2tvb70o71...@mail.gmail.com>
> >>> Content-Type: text/plain; charset=UTF-8
> >>>
> >>> Dear Yasser,
> >>>
> >>> I am by no means an expert on hardware, but I would strongly advise
> against
> >>> buying a laptop for the specific purpose of running (any and all) MD
> >>> simulations. A desktop is much better suited platform for such a task,
> as
> >>> you should be able to get a much bigger bang for your buck (this is the
> >>> main reason, but there are more cons).
> >>>
> >>> Notice that I am not saying that you cannot run MD simulations on a
> laptop,
> >>> I'm just advising against it. In fact, you could probably run MD
> >>> simulations on a smartphone if you wanted to, but it doesn't sound
> like a
> >>> very good investment of your time and money. In my *personal opinion*,
> the
> >>> same holds true for the laptop.
> >>>
> >>> Best regards,
> >>> /J
> >>>
> >>> On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
> >>> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
> >>>
>  Hi all,
> 

Re: [gmx-users] Nstlist and constrain simulations

[Szilárd Páll]

--
Szilárd


On Tue, Feb 2, 2016 at 4:23 PM, Mark Abraham  wrote:
> Hi,
>
> On Tue, Feb 2, 2016 at 1:11 PM Michail Palaiokostas Avramidis <
> m.palaiokos...@qmul.ac.uk> wrote:
>
>> Hi Mark and thank you for your answer.
>> Please see below :)
>>
>> On 01/02/16 18:28, Mark Abraham wrote:
>> > Hi,
>> >
>> > On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis <
>> > m.palaiokos...@qmul.ac.uk> wrote:
>> >
>> >> Dear GMX users,
>> >>
>> >>
>> >> I would like to ask about your opinion on the size of the neighbour list
>> >> (nstlist).
>> >>
>> >>
>> >> I am running constraint simulations
>> >
>> > What do you mean by a "constraint simulation?"
>> Sorry, I should have been clearer. I am using the z-constraint method in
>> which I constrain the permeant along the z-axis in various positions and
>> I record the constraint force. Similar to umbrella sampling but with
>> constrained distances between the permeant and membrane.
>>
>
> Using which GROMACS feature? e.g. freeze groups and NPT are usually an
> unhappy combination.
>
>
>> >> of a permeant along a lipid bilayer. In the initial setup the system
>> runs
>> >> on NPT and nstlist 10 (which GROMACS changes to 40 automatically). With
>> >> this setup my simulation is very fast but always crashes at various
>> points
>> >> with the same way always. Initially it gives some LINCS warnings and
>> then
>> >> it gives an error that a particle "communicated to PME rank 2 are more
>> than
>> >> 2/3 times the cut-off out of the domain decomposition cell".
>> >>
>> > Usually this indicates your setup is unstable e.g. see
>> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up. I'll
>> proceed
>> > by assuming you're very confident that your membrane system has had a
>> > suitable few dozen+ nanoseconds of equilibration ;-)
>> Yes absolutely confident. The system does not crash with unconstrained
>> simulations. The membrane-solvent system is well equilibrated for 1μs
>> and then, after I introduce the permeant, I perform an energy
>> minimization and a short 500ps NPT-Berendsen equilibration to relax the
>> pressure that the permeant might have introduced.
>>
>
> I'd be skeptical that 500ps was enough.
>
>
>> > When I see the last pdb steps before crash, sometimes there seem to be
>> >> overlaps between the permeants and the lipids and then system explosions
>> >> and PBChaos. Other times it is not so dramatic.
>> >>
>> >>
>> >> So the question is, should I be conservative with the nstlist? When I
>> run
>> >> NPT simulations and change the nstlist to 1, the system does not fail.
>> >> Alternatively, if I change to NVT and nstlist to 10, again the system
>> runs
>> >> successfully. But NVT and 40 crashes.
>> >>
>> > This might all be a wild goose chase. If you are pulling permeants into
>> the
>> > membrane, then that creates pressure on the membrane and perhaps
>> > destabilizes the pressure coupling. If that's with Parrinello-Rahman then
>> > it can easily oscillate out of control, ending up violating the
>> assumptions
>> > under which the code is written.
>> Yes, this is why I run an small equilibration in the beginning. And to
>> be honest, technically, I do not pull the permeants. For each position,
>> I add it to the system in VMD, and then run the
>> minimization-equilibration-production sequence.
>> >
>> > Since GROMACS was doing the nstlist update automatically, I thought it
>> was
>> >> a "safe" option. Based on the above,however, I believe that since the
>> >> simulation runs with constraints, the system is more sensitive and thus
>> the
>> >> nstlist should be smaller. Can anyone validate that my hypothesis is
>> >> correct?
>> >>
>> > On the limited evidence available, I think your observations are more
>> > likely to be symptoms of the problem than the problem itself. How does
>> e.g.
>> > one permeant molecule behave?
>> Once again sorry for not being clear. The plural in permeants comes from
>> the fact that I test several molecules (e.g. water, ammonia etc) but it
>> is only one per simulation/system.
>>
>> So, you think that the updating of neighbour list, shouldn't affect the
>> problem?
>>
>
> Yep. You can force mdrun to use an nstlist of your choosing with mdrun
> -nstlist n. I would expect you to observe similar instability in such
> cases. The only case in which I think nstlist could matter is when
> something else is so badly wrong that particles diffuse further than the
> automated buffer anticipates, in which case any reduction of nstlist that
> keeps the simulation running is merely deferring the problem to analysis
> time...

Good point. However, I think that could be the case only if the error
in the estimate would cause several orders of magnitude increase in
drift. The larger nstlist, the more the Verlet buffer calculation
tends to over-estimate the buffer (i.e. err on the safe side). Hence,
the missed interactions would need to have a very large drift
contribution to be able to cancel the effect 

Re: [gmx-users] Nstlist and constrain simulations

[Szilárd Páll]

--
Szilárd


On Tue, Feb 2, 2016 at 3:34 PM, Michail Palaiokostas Avramidis
 wrote:
>
>
> On 02/02/16 14:04, Szilárd Páll wrote:
>> On Tue, Feb 2, 2016 at 11:17 AM, Michail Palaiokostas Avramidis
>>  wrote:
>>> Hi Mark and thank you for your answer.
>>> Please see below :)
>>>
>>> On 01/02/16 18:28, Mark Abraham wrote:
 Hi,

 On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis <
 m.palaiokos...@qmul.ac.uk> wrote:

> Dear GMX users,
>
>
> I would like to ask about your opinion on the size of the neighbour list
> (nstlist).
>
>
> I am running constraint simulations
 What do you mean by a "constraint simulation?"
>>> Sorry, I should have been clearer. I am using the z-constraint method in
>>> which I constrain the permeant along the z-axis in various positions and
>>> I record the constraint force. Similar to umbrella sampling but with
>>> constrained distances between the permeant and membrane.
> of a permeant along a lipid bilayer. In the initial setup the system runs
> on NPT and nstlist 10 (which GROMACS changes to 40 automatically). With
> this setup my simulation is very fast but always crashes at various points
> with the same way always. Initially it gives some LINCS warnings and then
> it gives an error that a particle "communicated to PME rank 2 are more 
> than
> 2/3 times the cut-off out of the domain decomposition cell".
>
 Usually this indicates your setup is unstable e.g. see
 http://www.gromacs.org/Documentation/Terminology/Blowing_Up. I'll proceed
 by assuming you're very confident that your membrane system has had a
 suitable few dozen+ nanoseconds of equilibration ;-)
>>> Yes absolutely confident. The system does not crash with unconstrained
>>> simulations. The membrane-solvent system is well equilibrated for 1μs
>>> and then, after I introduce the permeant, I perform an energy
>>> minimization and a short 500ps NPT-Berendsen equilibration to relax the
>>> pressure that the permeant might have introduced.
 When I see the last pdb steps before crash, sometimes there seem to be
> overlaps between the permeants and the lipids and then system explosions
> and PBChaos. Other times it is not so dramatic.
>
>
> So the question is, should I be conservative with the nstlist? When I run
> NPT simulations and change the nstlist to 1, the system does not fail.
> Alternatively, if I change to NVT and nstlist to 10, again the system runs
> successfully. But NVT and 40 crashes.
>
 This might all be a wild goose chase. If you are pulling permeants into the
 membrane, then that creates pressure on the membrane and perhaps
 destabilizes the pressure coupling. If that's with Parrinello-Rahman then
 it can easily oscillate out of control, ending up violating the assumptions
 under which the code is written.
>>> Yes, this is why I run an small equilibration in the beginning. And to
>>> be honest, technically, I do not pull the permeants. For each position,
>>> I add it to the system in VMD, and then run the
>>> minimization-equilibration-production sequence.
 Since GROMACS was doing the nstlist update automatically, I thought it was
> a "safe" option. Based on the above,however, I believe that since the
> simulation runs with constraints, the system is more sensitive and thus 
> the
> nstlist should be smaller. Can anyone validate that my hypothesis is
> correct?
>
 On the limited evidence available, I think your observations are more
 likely to be symptoms of the problem than the problem itself. How does e.g.
 one permeant molecule behave?
>>> Once again sorry for not being clear. The plural in permeants comes from
>>> the fact that I test several molecules (e.g. water, ammonia etc) but it
>>> is only one per simulation/system.
>>>
>>> So, you think that the updating of neighbour list, shouldn't affect the
>>> problem?
>> No, it should not; for details see manual section 3.4.2.
>>
>> What GROMACS version are you using?
>
> I am using GROMACS 5.1.1
>
> The thing is that I see a difference on the stability when I change
> nstlist. In fact it is not crashing when I reduce the nstlist. And to be
> honest intuitively it should affect it.

That's if you ignore the automated pair-list buffer estimation.

> Anyway I looked at the manual
> but I couldn't see anything directly related to the question posed here.

Perhaps the documentation is not explicit enough about it, but with
the Verlet scheme implementation, as a pair list buffer is
automatically determined for the simulated system and setting in
question (rather than based on a rule of thumb like in the group
scheme or using an insanely conservative invalidation criteria other
packages use). Hence, nstlist becomes merely an
performance-optimization parameter and it won't affect energy
conservation.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Szilárd Páll]

Hi,

What exactly do you want from the laptop besides performance?
Autonomy, weight, size restrictions?

If you want something with a decent amount of autonomy, just get a
high-end Skylake laptop and do your runs on your workstation or
cluster. If you care about battery time, you may as well forget about
a powerful system (even a standalone GPU may not be worth it unless
you can get switchable graphics) - or at least plan to put effort into
avoiding high CPU/GPU load when on battery.

If you want max performance, get a beast that's often referred to as
"portable workstation" with a high-performance CPU (not 15W part) and
a GTX 970M or 980M. AFAIK NVIDIAs site has a section where they
advertise gaming laptops with these high-end mobile chips.

Unless you want to suffer with Windows, I'd also recommend looking
around before buying and making sure that you don't end up with some
niche hardware that does not run well under GNU/Linux. I can highly
recommend System76, they have some monsters too - I have even seen
recently a rave review about a portable workstation they offer with a
desktop CPU.

Cheers,
--
Szilárd



On Wed, Feb 3, 2016 at 11:17 AM, Yasser Almeida Hernández
 wrote:
> Dear Joao,
>
> I am aware that laptops are not the proper hardware to run MD simulations. I
> do my runs in workstations designed for that purpose. The hardware I want to
> buy is not just for simulations, but for general private/work purpose, but I
> would like to have a device robust enough to run calculations. My question
> was to get some thoughts about an ideal/optimal hardware.
>
> Best
>
> Yasser
>
> 
> Message: 6
> Date: Wed, 3 Feb 2016 10:53:31 +0100
> From: Jo?o Henriques 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Laptop features for MD simulations -
> recommendations
> Message-ID:
> 
> Content-Type: text/plain; charset=UTF-8
>
> Dear Yasser,
>
> I am by no means an expert on hardware, but I would strongly advise against
> buying a laptop for the specific purpose of running (any and all) MD
> simulations. A desktop is much better suited platform for such a task, as
> you should be able to get a much bigger bang for your buck (this is the
> main reason, but there are more cons).
>
> Notice that I am not saying that you cannot run MD simulations on a laptop,
> I'm just advising against it. In fact, you could probably run MD
> simulations on a smartphone if you wanted to, but it doesn't sound like a
> very good investment of your time and money. In my *personal opinion*, the
> same holds true for the laptop.
>
> Best regards,
> /J
>
> On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
>
>> Hi all,
>>
>> I want to buy a laptop suitable and powerful enough for MD simulations
>> with GROMACS (mostly membrane/protein systems). Could you recommend
>> optimal
>> features for this goal?
>>
>> Thanks
>>
>> Yasser
>>
>> --
>> Yasser Almeida Hern?ndez
>> PhD student
>> Institute of Biochemistry and Molecular Biology
>> Department of Chemistry
>> University of Hamburg
>> Martin-Luther-King-Platz 6
>> 20146 Hamburg
>> Germany
>> +49 40 42838 2845
>> yasser.almeida.hernan...@chemie.uni-hamburg.de
>> office: Grindelallee 117, room 250c
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
> --
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 142, Issue 14
> **
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe 

[gmx-users] Fwd: FW: PME settings in free energy calculations

[Michael Shirts]

Hi, Dries-

Questions like this are probably best answered on the gmx-users list.
I can't say too much for the Verlet scheme -- I know that it was
relatively recently adapted for free energies, and there may be some
combinations of settings that could give unanticipated results.

Pretty much all of our experience about nonbonded calculations and
free energies is collected in the following paper:
http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used the group
cutoff scheme since that was the only one that was supported in
GROMACS at the time.

Since you haven't sent any files, it's hard to tell what is actually
going on. The one thing that has a tendency to happen with the more
recent update schemes is if you set a potential modifier that is a
switch, but don't set the distance the switch starts at, then it is
automatically set to zero.  Check the mdout.mdp to see if this is
happening.

> From: Van Rompaey Dries 
Date: Wednesday, February 3, 2016 at 12:34 PM
To: Michael Shirts 
Subject: PME settings in free energy calculations

Dear prof. Shirts,

I'm currently trying to figure out the PME settings for a relative
free binding energy simulation I'm working on. I took the parameters
from Matteo Aldeghi's
paper(http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc02678d#!divAbstract)
as a starting point (adapted for the Verlet scheme by scaling the
fourierspacing to 0.08 and setting coulomb = rvdw = 1.0). I then tried
to verify these settings by comparing a single point energy
calculation with these settings and one with very long coulomb cutoffs
as recommended on alchemistry.org.

Unfortunately, I can't seem to get this quite right. I'm getting
differences in the hundreds of kj/mol, leading me to suspect I'm doing
something wrong. I'm calculating the energy values by extracting
CoulombSR and Coul-recip from the energy.xvg files. I've tried
calculating the energy with coulomb cutoffs at 3 nm and 10 nm, but
agreement with the PME results remains rather poor. David Mobley
mentioned you performed extensive research on this topic, and I'm
hoping you could point me in the right direction.

Thanks in advance,

Dries




Michael Shirts
Associate Professor
michael.shi...@colorado.edu
Phone: (303) 735-7860
Office: JSCBB D317
Department of Chemical and Biological Engineering
University of Colorado Boulder
-- 
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.

[gmx-users] C_v and Temperature

[Alexander Alexander]

Dear Gromacs user,

Normally there is a "*ref-t" [K]  *in .mdp file as reference temperature in
NVT calculation, in addition, yet another Temperature must be indicated in
"gmx dos *-T* XXX ..." for example in heat capacity (C_v) calculation with
quantum correction. So, I was wondering that which of these two
temperatures is the one that the heat capacity (C_v) has been calculated in
to be reported later?

One more question:
In C_v calculation, would you please confirm me that the "gmx dos" would
give only the quantum correction for C_v? Not the total C_v including
quantum correction.
IF so, then, the Total C_v  would be:
Total C_v = "gmx energy -nmol -fluct_props" + "gmx dos -T ..."

Thank you so much.

Cheers,

Alex
-- 
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.

[gmx-users] Free energy calculations with tabulated potentials

[POTTER T.D.]

Hi,

I've been running free energy calculations using the BAR method on Gromacs 
4.6.7 for my coarse-grained system, which uses numerical tabulated potentials 
for the bonded and non-bonded interactions. I get good agreement for free 
energies between my coarse-grained and atomistic systems, but I can't seem to 
find specifically how it works for tabulated potentials. If I have my 
interaction fully turned on at lambda=0, and fully turned off at lambda=1, how 
does Gromacs calculate the potential at intermediate lambdas?

Thanks,
Tom
-- 
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.

Re: [gmx-users] C_v and Temperature

[David van der Spoel]

On 03/02/16 23:52, Alexander Alexander wrote:

Dear Gromacs user,

Normally there is a "*ref-t" [K]  *in .mdp file as reference temperature in
NVT calculation, in addition, yet another Temperature must be indicated in
"gmx dos *-T* XXX ..." for example in heat capacity (C_v) calculation with
quantum correction. So, I was wondering that which of these two
temperatures is the one that the heat capacity (C_v) has been calculated in
to be reported later?

To get the simulation temperature run gmx energy



One more question:
In C_v calculation, would you please confirm me that the "gmx dos" would
give only the quantum correction for C_v? Not the total C_v including
quantum correction.
IF so, then, the Total C_v  would be:
Total C_v = "gmx energy -nmol -fluct_props" + "gmx dos -T ..."

Have you checked the output from gxm dos?
It describes everything in quite some detail.


Thank you so much.

Cheers,

Alex




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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.

Re: [gmx-users] trjconv - two chains are separated

[Peter Stern]

I have also encountered this problem and was able to solve it using the tpr 
file generated before running editconf as the input to trjconv (with -pbc no 
jump).

Peter

Sent from my iPad

> On 3 בפבר׳ 2016, at 4:51, Catarina A. Carvalheda dos Santos 
>  wrote:
> 
> Hi there,
> 
> I had similar problems in the past. You'll have to play with trjconv and
> find the best combination of different flags to solve the visualization
> problem.
> 
> You can start by trying out this workflow for example:
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> Hope this helps.
> 
> Good luck!
> 
> 
> 
> On 3 February 2016 at 06:15, Trayder Thomas 
> wrote:
> 
>> For "-pbc nojump" to work, you need to make sure they are together (as you
>> want) in the first frame of your input trajectory.
>> 
>> The most reliable way to do this is by centering the trajectory on a
>> residue at the interface between the two chains (using a custom index
>> group).
>> 
>> I've also heard some people have had luck with "-pbc cluster"
>> 
>> You can then run "-pbc nojump" on the centered (or clustered) trajectory.
>> 
>> -Trayder
>> 
>> 
>> 
>> 
>>> On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu  wrote:
>>> 
>>> Hi Gromacs Users,
>>> 
>>> I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my
>> trajectories.
>>> My protein has two chains (A and B) and they closely bind to each other.
>>> after running trjconv with "-pbc nojump", two chains are greatly
>> separated
>>> by a certain distance. It is mostly likely that the pbc is not
>> successfully
>>> removed and the program takes a chain from one unit cell and another from
>>> another unit cell.
>>> 
>>> Does anybody have any idea to solve the problem?
>>> 
>>> Best
>>> Yunlong
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>> 
>> The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> 
> 
> -- 
> Catarina A. Carvalheda
> 
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] CNT using g_x2top

[soumadwip ghosh]

Hi,
   previously I had a query about making the topology of CNT using g_x2top
in connection with charmm force field. I have followed Justin's advice and
was able to generate a 9X9 SWCNT in charmm which I want to simulate with a
single stranded DNA.  During energy minimization I got this error.

Reading file em.tpr, VERSION 4.5.6 (single precision)
Starting 80 threads
There were 36 inconsistent shifts. Check your topology
There were 36 inconsistent shifts. Check your topology

Will use 56 particle-particle and 24 PME only nodes
This is a guess, check the performance at the end of the log file

---
Program mdrun, VERSION 4.5.6
Source code file: domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 56 nodes that is compatible with the
given box and a minimum cell size of 8.21617 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Is there a problem with the topology or the gromacs 4.5.6 is unable to
perform the domain decomposition? If the second is the case can I play
around with mdrun options to get rid of this. I have seen this question
posted on the forum multiple times but I dint get any idea of
troubleshooting it in my case. I tried playing with -nt 1 in which mdrun
prints a number of .pdb files and the output.gro file contains a broken
CNT. I have attaced the log file, the cnt.itp file and the minim.mdp file.
Please let me know if the problem can be settled or the cnt.top itself is
faulty.

https://drive.google.com/file/d/0B7SBnQ5YXQSLd1d1cGtSRGZkUE0/view?usp=sharing
for
the em.log file

https://drive.google.com/file/d/0B7SBnQ5YXQSLWjFab1NIMmFiQVk/view?usp=sharing
for
the cnt.itp file and

https://drive.google.com/file/d/0B7SBnQ5YXQSLd3gtRFFrTTA4Wlk/view?usp=sharing
for
the minim.mdp file.

Any kind of help will be hugely appreciated.

Regards,
Soumadwip Ghosh
Senior Research Fellow
IITB
India
-- 
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.

Re: [gmx-users] CNT using g_x2top

[Mark Abraham]

If a single domain doesn't work, then surely your topology or starting
configuration is broken. Start with the simplest system you fan think of!

Mark

On Wed, 3 Feb 2016 17:23 soumadwip ghosh  wrote:

> Hi,
>previously I had a query about making the topology of CNT using g_x2top
> in connection with charmm force field. I have followed Justin's advice and
> was able to generate a 9X9 SWCNT in charmm which I want to simulate with a
> single stranded DNA.  During energy minimization I got this error.
>
> Reading file em.tpr, VERSION 4.5.6 (single precision)
> Starting 80 threads
> There were 36 inconsistent shifts. Check your topology
> There were 36 inconsistent shifts. Check your topology
>
> Will use 56 particle-particle and 24 PME only nodes
> This is a guess, check the performance at the end of the log file
>
> ---
> Program mdrun, VERSION 4.5.6
> Source code file: domdec.c, line: 6436
>
> Fatal error:
> There is no domain decomposition for 56 nodes that is compatible with the
> given box and a minimum cell size of 8.21617 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Is there a problem with the topology or the gromacs 4.5.6 is unable to
> perform the domain decomposition? If the second is the case can I play
> around with mdrun options to get rid of this. I have seen this question
> posted on the forum multiple times but I dint get any idea of
> troubleshooting it in my case. I tried playing with -nt 1 in which mdrun
> prints a number of .pdb files and the output.gro file contains a broken
> CNT. I have attaced the log file, the cnt.itp file and the minim.mdp file.
> Please let me know if the problem can be settled or the cnt.top itself is
> faulty.
>
>
> https://drive.google.com/file/d/0B7SBnQ5YXQSLd1d1cGtSRGZkUE0/view?usp=sharing
> for
> the em.log file
>
>
> https://drive.google.com/file/d/0B7SBnQ5YXQSLWjFab1NIMmFiQVk/view?usp=sharing
> for
> the cnt.itp file and
>
>
> https://drive.google.com/file/d/0B7SBnQ5YXQSLd3gtRFFrTTA4Wlk/view?usp=sharing
> for
> the minim.mdp file.
>
> Any kind of help will be hugely appreciated.
>
> Regards,
> Soumadwip Ghosh
> Senior Research Fellow
> IITB
> India
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Dries Van Rompaey]

Hi,

Just to expand a bit on Szilárd’s excellent answer, you can find a list of 
benchmarks for mobile cards here:
http://www.notebookcheck.net/Mobile-Graphics-Cards-Benchmark-List.844.0.html

Kind regards

Dries


> On 03 Feb 2016, at 15:14, Szilárd Páll  wrote:
> 
> Hi,
> 
> What exactly do you want from the laptop besides performance?
> Autonomy, weight, size restrictions?
> 
> If you want something with a decent amount of autonomy, just get a
> high-end Skylake laptop and do your runs on your workstation or
> cluster. If you care about battery time, you may as well forget about
> a powerful system (even a standalone GPU may not be worth it unless
> you can get switchable graphics) - or at least plan to put effort into
> avoiding high CPU/GPU load when on battery.
> 
> If you want max performance, get a beast that's often referred to as
> "portable workstation" with a high-performance CPU (not 15W part) and
> a GTX 970M or 980M. AFAIK NVIDIAs site has a section where they
> advertise gaming laptops with these high-end mobile chips.
> 
> Unless you want to suffer with Windows, I'd also recommend looking
> around before buying and making sure that you don't end up with some
> niche hardware that does not run well under GNU/Linux. I can highly
> recommend System76, they have some monsters too - I have even seen
> recently a rave review about a portable workstation they offer with a
> desktop CPU.
> 
> Cheers,
> --
> Szilárd
> 
> 
> 
> On Wed, Feb 3, 2016 at 11:17 AM, Yasser Almeida Hernández
>  wrote:
>> Dear Joao,
>> 
>> I am aware that laptops are not the proper hardware to run MD simulations. I
>> do my runs in workstations designed for that purpose. The hardware I want to
>> buy is not just for simulations, but for general private/work purpose, but I
>> would like to have a device robust enough to run calculations. My question
>> was to get some thoughts about an ideal/optimal hardware.
>> 
>> Best
>> 
>> Yasser
>> 
>> 
>> Message: 6
>> Date: Wed, 3 Feb 2016 10:53:31 +0100
>> From: Jo?o Henriques 
>> To: Discussion list for GROMACS users 
>> Subject: Re: [gmx-users] Laptop features for MD simulations -
>>recommendations
>> Message-ID:
>>
>> Content-Type: text/plain; charset=UTF-8
>> 
>> Dear Yasser,
>> 
>> I am by no means an expert on hardware, but I would strongly advise against
>> buying a laptop for the specific purpose of running (any and all) MD
>> simulations. A desktop is much better suited platform for such a task, as
>> you should be able to get a much bigger bang for your buck (this is the
>> main reason, but there are more cons).
>> 
>> Notice that I am not saying that you cannot run MD simulations on a laptop,
>> I'm just advising against it. In fact, you could probably run MD
>> simulations on a smartphone if you wanted to, but it doesn't sound like a
>> very good investment of your time and money. In my *personal opinion*, the
>> same holds true for the laptop.
>> 
>> Best regards,
>> /J
>> 
>> On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
>> yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:
>> 
>>> Hi all,
>>> 
>>> I want to buy a laptop suitable and powerful enough for MD simulations
>>> with GROMACS (mostly membrane/protein systems). Could you recommend
>>> optimal
>>> features for this goal?
>>> 
>>> Thanks
>>> 
>>> Yasser
>>> 
>>> --
>>> Yasser Almeida Hern?ndez
>>> PhD student
>>> Institute of Biochemistry and Molecular Biology
>>> Department of Chemistry
>>> University of Hamburg
>>> Martin-Luther-King-Platz 6
>>> 20146 Hamburg
>>> Germany
>>> +49 40 42838 2845
>>> yasser.almeida.hernan...@chemie.uni-hamburg.de
>>> office: Grindelallee 117, room 250c
>>> 
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>> 
>> 
>> 
>> --
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
>> mail to gmx-users-requ...@gromacs.org.
>> 
>> End of gromacs.org_gmx-users Digest, Vol 142, Issue 14
>> **
>> 
>> 
>> 
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> 

Re: [gmx-users] How to visualizing gro file in pymol

[Francesco Carbone]

I use to have the same problem and in my case it was cause by the fact that
I was using a different tpr file (cleaned from water).
When I started using the "untouched" tpr file (the one used during the
simulation) everything went fine using trjconv and the -dump option.

Fra

On 3 February 2016 at 10:43, Catarina A. Carvalheda dos Santos <
c.a.c.dossan...@dundee.ac.uk> wrote:

> Hi Anu,
>
> You can always use ediconf to convert your .gro file into a .pdb file =)
>
> For multiple chain systems Pymol needs the chain information in the
> structure file. Because .gro files don't have the chain info, you'll always
> need a .pdb file.
> If this is your case, that's the reason why the cartoon representation
> isn't working.
>
> Hope this helps,
>
> Cheers,
>
> On 3 February 2016 at 10:33, anu chandra  wrote:
>
> > Hello all,
> >
> > I just finished a short simulation of a membrane protein system and
> trying
> > to visualize the final gro file generated from the simulation using
> Pymol.
> > Unfortunately, the Pymol failed to visualize the protein in cartoon
> > representation. Though VMD can do the job, I just wonder is there a way I
> > can visualize the gro file in Pymol. A quick surfing on web suggested to
> > use the editconf to convert the .tpr file to .pdb file for visualizing
> with
> > Pymol. Unfortunately, here the .tpr file have structural information from
> > the beginning of the simulation rather than at the end of the simulation.
> >
> >
> > Any suggestion would be very much appreciated.
> >
> >
> > Many thanks
> > Anu
> > --
> > 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.
> >
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> >
>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.