Re: [gmx-users] Ignoring H-atoms.

[Amir Zeb]

Hello Maria,

f igoring h-atom command is applied ,,then forcefield will ignore all the
added h-atoms

What I know about -ignh flag, it does not mean to remove the h-atoms,
alternatively means that during the topology generation, the force field is
considering the h-atoms as the light atoms and does not pay much attention
to consider their parameters so accurately.

it would be a vaccum simulation if
the h-atom will be ignored

Also, in case of vacuum simulation, I think there is no water addition,
while here we are gonna adding the water during the salvation step  of the
procedure. So, I think you don't need to worry about it.

At the end, I would like to appraise in deep the explanation of other users.

Cheers!

Amir

On Mon, Feb 6, 2017 at 10:12 PM, maria khan 
wrote:

> Dear Gromacs users,,
>
> if igoring h-atom command is applied ,,then forcefield will ignore all the
> added h-atoms,,,so my question is then it would be a vaccum simulation if
> the h-atom will be ignored,,secondly the results will be also differnt then
> when h-atoms are considered.
>
> Regards..
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[gmx-users] Ignoring H-atoms.

[maria khan]

Dear Gromacs users,,

if igoring h-atom command is applied ,,then forcefield will ignore all the
added h-atoms,,,so my question is then it would be a vaccum simulation if
the h-atom will be ignored,,secondly the results will be also differnt then
when h-atoms are considered.

Regards..
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[gmx-users] how to link connections to ligating residues

[Shumaila Khan]

Hello Sir,
        Hopefully you are doing well. As I am new to GROMACS, I am facing 
problems.
I read your comments and You suggested someone that "You should not need 
external servers to generate a heme topology; GROMOS already supports it.  It's 
called HEME and it's in the .rtp file.  Connections to
ligating residues should be recognized via existing entries in specbond.dat."
I am using
Version : 5.0.7
Force Feild : 43a1 Spc water model.
The  ligand  attached to heme is oxygen molecule.
HETATM 1  O1  OXY C1543      5.525  80.353  -6.212  1.00 25.38  O
HETATM 2  O2  OXY C1543      4.301  80.342  -6.721  1.00 30.35  O
END

The specbond.dat file contains the following:
8
CYS    SG    1    CYS    SG    1    0.2    CYS2    CYS2
CYS    SG    1    HEM    FE    2    0.25    CYS2    HEME
CYS    SG    1    HEM    CAB    1    0.18    CYS2    HEME
CYS    SG    1    HEM    CAC    1    0.18    CYS2    HEME
HIS    NE2    1    HEM    FE    1    0.2    HIS1    HEME
MET    SD    1    HEM    FE    1    0.24    MET    HEME
CO  C      1      HEME    FE      1      0.19    CO      HEME
CYM  SG      1      CYM    SG      1      0.2    CYS2    CYS2
 

Kindly please guide me, how connections to ligating residues should be 
recognized via existing entries in specbond.dat?

 I shall be very thankful to you.
                                                                        
Shumaila khan
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[gmx-users] How to connect ligating residues ??

[Mehreen Jan]

Hello Sir Justin,

>  Hope so you are doing well. Thanks a lot for your kind response. 
Thank you very much for your reply.

> Version : 5.0.7
> FF: 43a1 Spc water model.
>
> Your Suggestion:
> "You should not need external servers to generate a heme topology; GROMOS 
> already
> supports it.  It's called HEME and it's in the .rtp file.  Connections to
> ligating residues should be recognized via existing entries in specbond.dat."
>
> This oxygen molecule is attached as a ligand to heme.
> HETATM 1  O1  OXY C1543   5.525  80.353  -6.212  1.00 25.38  O
> HETATM 2  O2  OXY C1543   4.301  80.342  -6.721  1.00 30.35  O
> END
>
> Now my question is how connections to ligating residues should be recognized 
> via existing entries in specbond.dat.
>
> The specbond.dat file contains the following:
> 8
> CYSSG1CYSSG10.2CYS2CYS2
> CYSSG1HEM FE20.25CYS2HEME
> CYSSG1HEM CAB10.18CYS2HEME
> CYSSG1HEM CAC10.18CYS2HEME
> HISNE21HEM FE10.2HIS1HEME
> METSD1HEM FE10.24METHEME
> CO  C   1   HEMEFE  1   0.19CO  HEME
> CYM  SG  1   CYM SG  1   0.2 CYS2CYS2
>
> Waiting for your kind response. I shall be very thankful to you.
>   
> Mehreen Jan
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Re: [gmx-users] INDEX

[Subashini .K]

Hi,


Lot of thanks.

I'll implement it in the command line.


Thanks,

Subashini.K



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Erik Marklund 

Sent: Monday, February 6, 2017 6:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] INDEX

Dear Subashini,

You forgot to provide trjconv with the index file you created. Try gmx trjconv 
-n your_index_file.ndx …

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se

On 6 Feb 2017, at 13:06, Subashini .K 
> wrote:

Hi gromacs users,


I want to visualize the results of simulations using the command


gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb


Wish to see Protein and ligand simulations together in the pdb file.


But, when the command is given, we can either select protein group or ligand 
group


Before this was done,


The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt


However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in 
the movie.pdb file.


What to do?

Can someone help?


Thanks,

Subashini.K


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[gmx-users] how to connect ligating residues?

[Shumaila Khan]

Hello Sir,
        Hopefully you are doing well. As I am new to GROMACS, I am facing 
problems.
I read your comments and You suggested someone that "You should not need 
external servers to generate a heme topology; GROMOS already supports it.  It's 
called HEME and it's in the .rtp file.  Connections to
ligating residues should be recognized via existing entries in specbond.dat."
I am using
Version : 5.0.7
Force Feild : 43a1 Spc water model.
The  ligand  attached to heme is oxygen molecule.
HETATM 1  O1  OXY C1543      5.525  80.353  -6.212  1.00 25.38  O
HETATM 2  O2  OXY C1543      4.301  80.342  -6.721  1.00 30.35  O
END

The specbond.dat file contains the following:
8
CYS    SG    1    CYS    SG    1    0.2    CYS2    CYS2
CYS    SG    1    HEM    FE    2    0.25    CYS2    HEME
CYS    SG    1    HEM    CAB    1    0.18    CYS2    HEME
CYS    SG    1    HEM    CAC    1    0.18    CYS2    HEME
HIS    NE2    1    HEM    FE    1    0.2    HIS1    HEME
MET    SD    1    HEM    FE    1    0.24    MET    HEME
CO  C      1      HEME    FE      1      0.19    CO      HEME
CYM  SG      1      CYM    SG      1      0.2    CYS2    CYS2
 

Kindly please guide me, how connections to ligating residues should be 
recognized via existing entries in specbond.dat?

 I shall be very thankful to you.
                                                                        
Shumaila khan
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[gmx-users] How to connect ligating residues ??

[Mehreen Jan]

 Hello,
>  Hope so you are doing well. Thanks a lot for your kind response.
> Version : 5.0.7
> FF: 43a1 Spc water model.
>
> Your Suggestion:
> "You should not need external servers to generate a heme topology; GROMOS 
> already
> supports it.  It's called HEME and it's in the .rtp file.  Connections to
> ligating residues should be recognized via existing entries in specbond.dat."
>
> This oxygen molecule is attached as a ligand to heme.
> HETATM 1  O1  OXY C1543   5.525  80.353  -6.212  1.00 25.38  O
> HETATM 2  O2  OXY C1543   4.301  80.342  -6.721  1.00 30.35  O
> END
>
> Now my question is how connections to ligating residues should be recognized 
> via existing entries in specbond.dat.
>
> The specbond.dat file contains the following:
> 8
> CYSSG1CYSSG10.2CYS2CYS2
> CYSSG1HEM FE20.25CYS2HEME
> CYSSG1HEM CAB10.18CYS2HEME
> CYSSG1HEM CAC10.18CYS2HEME
> HISNE21HEM FE10.2HIS1HEME
> METSD1HEM FE10.24METHEME
> CO  C   1   HEMEFE  1   0.19CO  HEME
> CYM  SG  1   CYM SG  1   0.2 CYS2CYS2
>
> Waiting for your kind response. I shall be very thankful to you.
>   
> Mehreen Jan
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Re: [gmx-users] How to choose z component of two groups

[Мижээ Батсайхан]

Dear Justin,

Thank you very much for your reply.

I inspected the thickness.xvg. There are number of columns in this file, I
could not realize that which one is Z component of thickness.
I also got averaged values using -oav option. How can I get the averaged
values of Z component?


Best regards,

Mijiddorj



Dear gmx users,

I am performing analysis of membrane system. I would like to estimate
membrane thickness.

I toke following command:

gmx distance 0s topol.tpr -f traj.xtc -n selected_P.ndx -oav ave.xvg -oxyz
thickness.xvg


I do not know how to select z component of the two groups.

Is there any advice, please?


Have you inspected the contents of thickness.xvg? I suspect you'll find
exactlywhat you're looking 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)
706-7441http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Fw: modelling of calcium ions

[Mahboobeh Eslami]

Hi
Thank you for your answersI want to change ffnonbonded.itp file for calcium 
ions. Have nm and KJ/mol units been used for sigma and epsilon values in this 
file, respectively? I ask this question to ensure. On Monday, February 6, 
2017 11:59 AM, Mahboobeh Eslami  wrote:
 

 I thank you for your answer.I want to change ffnonbonded.itp file for calcium 
ions. Have nm and KJ/mol units been used for sigma and epsilon values in this 
file, respectively? I ask this question to ensure.

Thank you so much
Best wishes  
 

On Sunday, February 5, 2017 9:29 PM, Christopher Neale 
 wrote:
 

 The things you'll have to be most careful of include whether the calcium ion 
parameters you choose can get the correct coordination states (as I recall, 
Calcium's coordination can be quite variable experimentally, in contrast to 
something like magnesium, which has a more strict coordination number). You can 
check this possibly by putting a calcium ion in water and integrating the RDF 
over the first shell, etc (or, obviously reading the literature about 
simulations with those ca2+ parameters). In addition, you might have to think 
about getting the right chi rotamers of asn and gln if they assist coordination 
(they are not always correct in crystal structures) and protonation states of 
coordinating side chains. For example, I am not sure if His can help to 
coordinate calcium, but if it can then you'll want to have the right tautomer 
(protonation on the epsilon vs delta nitrogen atom), etc.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 05 February 2017 11:18:10
To: gmx-us...@gromacs.org; Mahboobeh Eslami
Subject: Re: [gmx-users] modelling of calcium ions

On 2/5/17 4:18 AM, Mahboobeh Eslami wrote:
> Hi all GMX usersI hope you are wellI want to simulate a protein-ligand 
> complex. There are two calcium ions in the crystallographic structure of 
> protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I 
> use these parameter for modelling of calcium ions.? Please guide me.ThanksBest
>

Ca2+ is already present in every force field in GROMACS.  pdb2gmx should handle
it out of the box as long as the residue is named appropriately.  If you have
(good) reason to change any aspects of the parameters, you'll have to alter
ffnonbonded.itp to change the attributes of the corresponding atom type.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] modelling of calcium ions

[Justin Lemkul]

On 2/6/17 1:15 PM, Mahboobeh Eslami wrote:



 On Monday, February 6, 2017 11:59 AM, Mahboobeh Eslami 
 wrote:


 Hi
Thank you for your answersI want to change ffnonbonded.itp file for calcium 
ions. Have nm and KJ/mol units been used for sigma and epsilon values in this 
file, respectively? I ask this question to ensure.Thank you so much


Yes.  See Chapter 2 of the manual for the units GROMACS uses for everything.

-Justin


Best wishes


On Sunday, February 5, 2017 9:29 PM, Christopher Neale 
 wrote:


 The things you'll have to be most careful of include whether the calcium ion 
parameters you choose can get the correct coordination states (as I recall, 
Calcium's coordination can be quite variable experimentally, in contrast to 
something like magnesium, which has a more strict coordination number). You can 
check this possibly by putting a calcium ion in water and integrating the RDF 
over the first shell, etc (or, obviously reading the literature about 
simulations with those ca2+ parameters). In addition, you might have to think 
about getting the right chi rotamers of asn and gln if they assist coordination 
(they are not always correct in crystal structures) and protonation states of 
coordinating side chains. For example, I am not sure if His can help to 
coordinate calcium, but if it can then you'll want to have the right tautomer 
(protonation on the epsilon vs delta nitrogen atom), etc.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 05 February 2017 11:18:10
To: gmx-us...@gromacs.org; Mahboobeh Eslami
Subject: Re: [gmx-users] modelling of calcium ions

On 2/5/17 4:18 AM, Mahboobeh Eslami wrote:

Hi all GMX usersI hope you are wellI want to simulate a protein-ligand complex. 
There are two calcium ions in the crystallographic structure of protein. I want 
to keep them. I find non-bonded parameters of Ca+2. How can I use these 
parameter for modelling of calcium ions.? Please guide me.ThanksBest



Ca2+ is already present in every force field in GROMACS.  pdb2gmx should handle
it out of the box as long as the residue is named appropriately.  If you have
(good) reason to change any aspects of the parameters, you'll have to alter
ffnonbonded.itp to change the attributes of the corresponding atom type.

-Justin

--
==

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

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

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

==
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--
==

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

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

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

==
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[gmx-users] modelling of calcium ions

[Mahboobeh Eslami]

 On Monday, February 6, 2017 11:59 AM, Mahboobeh Eslami 
 wrote:
 

 Hi
Thank you for your answersI want to change ffnonbonded.itp file for calcium 
ions. Have nm and KJ/mol units been used for sigma and epsilon values in this 
file, respectively? I ask this question to ensure.Thank you so much
Best wishes  
 

On Sunday, February 5, 2017 9:29 PM, Christopher Neale 
 wrote:
 

 The things you'll have to be most careful of include whether the calcium ion 
parameters you choose can get the correct coordination states (as I recall, 
Calcium's coordination can be quite variable experimentally, in contrast to 
something like magnesium, which has a more strict coordination number). You can 
check this possibly by putting a calcium ion in water and integrating the RDF 
over the first shell, etc (or, obviously reading the literature about 
simulations with those ca2+ parameters). In addition, you might have to think 
about getting the right chi rotamers of asn and gln if they assist coordination 
(they are not always correct in crystal structures) and protonation states of 
coordinating side chains. For example, I am not sure if His can help to 
coordinate calcium, but if it can then you'll want to have the right tautomer 
(protonation on the epsilon vs delta nitrogen atom), etc.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 05 February 2017 11:18:10
To: gmx-us...@gromacs.org; Mahboobeh Eslami
Subject: Re: [gmx-users] modelling of calcium ions

On 2/5/17 4:18 AM, Mahboobeh Eslami wrote:
> Hi all GMX usersI hope you are wellI want to simulate a protein-ligand 
> complex. There are two calcium ions in the crystallographic structure of 
> protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I 
> use these parameter for modelling of calcium ions.? Please guide me.ThanksBest
>

Ca2+ is already present in every force field in GROMACS.  pdb2gmx should handle
it out of the box as long as the residue is named appropriately.  If you have
(good) reason to change any aspects of the parameters, you'll have to alter
ffnonbonded.itp to change the attributes of the corresponding atom type.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] constraining CoM of two proteins individually

[Justin Lemkul]

On 2/6/17 10:06 AM, Irem Altan wrote:

Hi,

I have a system that consists of two proteins separated by a certain distance. 
I want to keep this distance constant by constraining the center of mass of the 
two proteins individually. How can I do this?



If you just want to maintain a distance, use a biasing potential via the pull 
code.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] Fwd: Gromacs+Drude+Plumed patch issue

[Justin Lemkul]

On 2/6/17 12:11 PM, Christian Jorgensen wrote:

Hello,

I'm trying to compile the drude clone of Gromacs 5.1.4 with Plumed 2
from the git directory.

So far, the patching works but it requires modifying some of the source
code.
Here's what my IT technician told me when he tried:

It is not patching and when we managed to patched by force(changing a few
parts of the code, which are not our job) does not compile.

has anyone experienced issues with this?



Never tried it.  The Drude branch is not official yet as I am still tinkering, 
so tread lightly if you're going to be hacking things (like PLUMED) that aren't 
tested.  The Drude code is a rather large change relative to a released branch 
that PLUMED is designed for.  The current Drude code will run with OpenMP but DD 
is broken due to an overhaul I've had to do.  It's about 90% fixed but I can't 
make any promises on a fully functional delivery date (we're also about to do a 
large force field upgrade, which has been taking most of my time).


-Justin

--
==

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

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

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

==
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[gmx-users] pull code Umbrella

[virginia miguel]

Hi All, I am trying to run a pulling md for umbrella sampling of the partition 
of  two organic molecules into the center of a bilayer using the following mdp 
options:  

  pull = umbrella
  pull_geometry    = cylinder
  pull_r1  = 1.4
  pull_r0  = 1.9
  pull_dim = N N Y
  pull_start   = yes  ; define initial COM distance > 0
  pull_init1   = x
  pull_init2   = x
  pull_ngroups = 2
  pull_group0  = DPP
  pull_group1  = UNO
  pull_group2  = DOS
  pull_vec1    = 0 0 1
  pull_vec2    = 0 0 1
  pull_nstxout = 1000
  pull_nstfout = 1000
  pull_rate1   = -0.001    ; 0.001 nm per ps = 1 nm per ns
  pull_k1  = 1000  ; kJ mol^-1 nm^-2  
  pull_rate2   = -0.001    ; 0.001 nm per ps = 1 nm per ns
  pull_k2  = 1000  ; kJ mol^-1 nm^-2  

 


the thing is that in three md steeps, the molecules are in the center of the 
bilayer, whe they are supposed to move 1 nm per ns ...I have used these options 
before but using pull_geometry=distance and had no trouble, but now I do not 
know what  am I doing wrong...if some one could give me a hint, I would 
appreciate it. Regards, Virginia. Dra. Virginia Miguel
Instituto de Investigaciones Biológicasy Tecnológicas (IIBYT) 
CONICET-UNC
Av.Velez Sarsfield 1611, 5016
Córdoba,ARGENTINA. 
TE: +54 351- 4344983+54 351- 4344983 (int.5)
FAX: +54-351-4334139

I arise in the morning torn between a desire to improve the world and a desire 
to enjoy the world. 
This makes it hard to plan the day. (E.B. White)
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Re: [gmx-users] Vibrational, rotational and translational energy

[David van der Spoel]

On 06/02/17 17:59, qasimp...@gmail.com wrote:

Dear users,

Is that possible to calculate/get the vibrational, rotational and translational 
energy of a protein per residue with GROMACS?

Total energy of a molecule physically consists of electronic, vibrational, 
rotational and translational parts. But GROMACS calculates only the bonded and 
non-bonded energies. How do the bonded and non-bonded energies represent the 
total energy of a system. I get confused :(

There is only total energy. Energy per residue has no physical meaning. 
However you can do a normal mode analysis of your protein and analyze 
the vibrational frequencies.




Thanks in advance.






--
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
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[gmx-users] Fwd: Gromacs+Drude+Plumed patch issue

[Christian Jorgensen]

Hello,

I'm trying to compile the drude clone of Gromacs 5.1.4 with Plumed 2
from the git directory.

So far, the patching works but it requires modifying some of the source
code.
Here's what my IT technician told me when he tried:

It is not patching and when we managed to patched by force(changing a few
parts of the code, which are not our job) does not compile.

has anyone experienced issues with this?

Thanks




Chris
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Re: [gmx-users] Periodicity in x-y plane (Neda Rafiee)

[Neda Rafiee]

Thanks Bjoern!

Kind regards,
Neda Rafieiolhosseini
Ph.D. Student at Institute for Research
in Fundamental Sciences(IPM),
School of Nano,
Tehran,Iran. 

- Original Message -
From: "Björn Sommer" 
To: "gromacs org gmx-users" 
Sent: Monday, February 6, 2017 2:43:21 PM
Subject: Re: [gmx-users] Periodicity in x-y plane (Neda Rafiee)

Hi Neda,

On 6/02/2017 8:43 am, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
wrote:
>6. Periodicity in x-y plane (Neda Rafiee)
>
>
>
> Message: 6
> Date: Mon, 6 Feb 2017 11:08:42 +0330 (IRST)
> From: Neda Rafiee 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Periodicity in x-y plane
> Message-ID: <12473704.8815.1486366722721.javamail.r...@zmail.ipm.ir>
> Content-Type: text/plain; charset=utf-8
>
> Hi. I have already built a lipid bilayer and I want to create a box for it 
> and fill it with water. I used : 
> $ gmx editconf -f renumber.gro -o newbox.gro  -c -box 8 8 14 -bt triclinic  
> and after that I used:
> $ gmx solvate -cp newbox.gro -cs tip4p.gro -o solvated.gro -p topol.top  
>
> but when I see solvated.gro in VMD, in periodicity , I check x +x or y +y 
> direction, I see man water molecules between adjacent neighbors in x-y 
> direction and it destroy the periodicity of my membrane in x-y plane, while I 
> want to have water only in the upper and lower sides of the membrane. What 
> should I do? 
>
>
Please play around with this:
http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=21=641

Shortly, in VMD use in the Graphical Representations window a selection like
not ((resname 'W' 'NA+') and within 5.5 of (not resname 'W' 'NA+'))

See the previous link for more info. Basically, make sure that no water
is inside the membrane but also that the distance between the water bath
and the head groups is not too small, otherwise the box will shrink
during simulation and the membrane might deform a little bit.

After that, use the regular PDB export and make sure to select the
actual selection in the export window!/
/
Have fun!
Bjorn
/
/
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[gmx-users] Vibrational, rotational and translational energy

[qasimpars]

Dear users,

Is that possible to calculate/get the vibrational, rotational and translational 
energy of a protein per residue with GROMACS? 

Total energy of a molecule physically consists of electronic, vibrational, 
rotational and translational parts. But GROMACS calculates only the bonded and 
non-bonded energies. How do the bonded and non-bonded energies represent the 
total energy of a system. I get confused :(

Thanks in advance.



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[gmx-users] constraining CoM of two proteins individually

[Irem Altan]

Hi,

I have a system that consists of two proteins separated by a certain distance. 
I want to keep this distance constant by constraining the center of mass of the 
two proteins individually. How can I do this? 

Best,
Irem
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Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

[Christopher Neale]

Dear Peter:

The reason that I can't use your suggestion (I think) was my specification that 
I don't want any coordinates to change at all (i.e., no bulk translation of 
molecule A while changing the periodic representation of molecule B). If I have 
misunderstood and one can really use trjconv -center or some similar command to 
do what I need then I'd appreciate an exact command and I'll try it out. Of 
course, I could use use trjconv -center, then figure out how much things had 
moved, then trjconv -translate to get it back, but I would like to avoid that 
(and if I had to go through such a procedure anyway I would rather simply 
compute how to move molecule B myself and then split it out and move it and 
rejoin it which I could do but wanted to avoid).

Thank you,
Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Kroon, P.C. 

Sent: 06 February 2017 04:10:28
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] how to reimage PBC based on distance to a given 
selection without recentering or otherwise changing atomic coordinates

Hi,

I don't have an example at hand, but I'll remember!
Thanks for the hard work :)

Peter

On Mon, Feb 6, 2017 at 10:08 AM, Mark Abraham 
wrote:

> Hi,
>
> If so, please share a case on https://redmine.gromacs.org that doesn't
> work
> as you think it should. We're very happy to make things work better!
>
> Mark
>
> On Mon, 6 Feb 2017 10:04 Kroon, P.C.  wrote:
>
> > Alternatively, center it on an interfacial residue. pbc cluster doesn't
> > always work, unfortunately.
> >
> > Peter
> >
> > On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
> > chris.ne...@alum.utoronto.ca> wrote:
> >
> > > Awesome Mark, thanks! It works.
> > >
> > > I filed a bug about a nonexistent -clustercenter option mentioned in
> the
> > > v5.1.2 help file, but the command seems to work anyway for my usage.
> > >
> > > Thanks again,
> > > Chris.
> > > 
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > > Abraham 
> > > Sent: 04 February 2017 07:27:52
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] how to reimage PBC based on distance to a
> given
> > > selection without recentering or otherwise changing atomic coordinates
> > >
> > > Hi,
> > >
> > > I've never really use it myself, but I imagine trjconv -pbc cluster is
> > > useful for this kind of scenario when you want to treat a group of
> > > molecules as indivisible.
> > >
> > > Mark
> > >
> > > On Sat, 4 Feb 2017 09:33 Christopher Neale <
> chris.ne...@alum.utoronto.ca
> > >
> > > wrote:
> > >
> > > > Dear users:
> > > >
> > > > I have a system in which molecule A is in direct contact with
> molecule
> > B.
> > > > However, molecule B is imaged in a different periodic cell. What I
> > would
> > > > like to do is to get an image of both molecules in a periodic
> > > > representation in which they actually are in contact (i.e., reimage
> > > > molecule B such that it is closest to molecule A). However, I do not
> > want
> > > > to lose spatial information with e.g. a trjconv -center -pbc mol
> > command.
> > > >
> > > > This is part of a complex automated build procedure and I can get
> into
> > > > more details if that is useful, but the crux is that I am extracting
> a
> > > > frame from a simulation, building more atoms onto molecule A, and
> > setting
> > > > up a new simulation. To build onto molecule A, I want to then do a
> > vacuum
> > > > EM before adding it back to the water box, for which I first enlarge
> > the
> > > > vacuum box, and changing box dimensions is messing with the
> periodicity
> > > and
> > > > throwing molecule B away from molecule A in an unrealistic fashion
> > > > (molecule B is a tightly bound ligand).
> > > >
> > > > I could do what I want by breaking each molecule out into its own
> box,
> > > > checking for contacts, reimaging, and then putting them back
> together.
> > I
> > > > presume (but have not checked) that I could also do this by making a
> > new
> > > > .itp file in which both molecule A and B are part of the same [
> > molecule
> > > ]
> > > > definition and then running a zero-step mdrun. However, I am writing
> to
> > > see
> > > > if anybody knows how reimage based on a selection (would be a single
> > atom
> > > > in molecule A near the contact between molecule A and B) more
> elegantly
> > > > with processing tools available in gromacs.
> > > >
> > > > Thank you for your help,
> > > > Chris.
> > > > --
> > > > 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 

Re: [gmx-users] Force field for Cobalt topology??

[Justin Lemkul]

On 2/6/17 9:08 AM, Amir Zeb wrote:

Hello gmx users,

I'm wondering which would be the best force field to create topology for
cobalt. I tried different ff but none of them get the task. I searched the
mailing archive too but I couldn't get the way to solve the issue.
Dr. Justin has just mentioned (https://www.mail-archive.com/gmx
us...@gromacs.org/msg46374.html) that there is no such suitable force field
yet to deal with transition metals correctly due to their lack of fixed
charge. But this was commented so back.
Let me know if the recent advances had solved such issue.



The link doesn't point to a valid page, so I don't know the context or content 
of that post, but I can probably guess :)  I may be repeating myself, but here goes:


Transition metals are challenging for additive MD force fields.  There are 
issues of polarization, charge transfer, and coordination (which can be flexible 
and ligand-dependent).  Additive MD force fields are quite crude in this regard 
and often can't capture such effects (heck, even "common" ions like Ca2+ and 
Mg2+ are often represented very poorly, let alone harder things like transition 
elements).  QM/MM may be a solution, in which you treat the cobalt and ligating 
residues as a QM region and the rest of the system as MM, but it depends on what 
you're doing as to whether or not you want to invest a lot of time in such an 
effort.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] Propylene Carbonate

[Justin Lemkul]

On 2/6/17 9:46 AM, Sencer Selcuk wrote:

Justin,

I am pretty sure there is a reliable parametrization of propylene carbonate (PC)
in OPLSaa. The OPLSaa parameters included in GROMACS lists all PC atoms
explicitly as well. The opls_771 to opls_779 non-bonded types correspond to PC
atoms.

In the bonded part, however, OS-C-OS angle is missing. I checked the parameters
provided with Tinker, the same angle is missing.  There are several papers &
dissertations where people say they used GROMACS and the OPLS parameters
provided there in to model PC. So I feel like none of the parameters are
missing, but  I am doing something wrong.



Contact those authors and ask for their topologies to see what they did.  Maybe 
they parametrized the angle and just forgot to mention that, or they used 
parameters from a similar angle (and forgot to mention that), or they used 
different types.  But if simulations of this molecule have been done before, 
avoid reinventing the wheel - this is why there are corresponding authors!


-Justin


I would really appreciate if you, or someone with experience can take a quick
look -as I believe this should be a very straight forward example of .top
generation.

Best,

Sencer


On Mon, Feb 6, 2017 at 7:41 AM, Justin Lemkul  wrote:



On 2/5/17 12:29 PM, Sencer Selcuk wrote:

Sotirios,

Thanks for your response. The angle I am looking at is actually present in the
molecule, but the corresponding parameters are missing from the ffbonded.itp.
With the hope that white spaces won't be messed when I send this email, this is
the propylene carbonate molecule with the bonded atom types listed in
ffnonbonded.itp:

O
||
C
   /  \
OS   OS
 |  |
CT---CT-CT


and the angle I cannot find in the ffbonded.itp is OS-C-OS bond.



If the force field doesn't already have parameters for it, you'll need to
parametrize it in accordance with the parent force field's normal
parametrization strategy.  There may be parameters in OPLS-AA that are
published but not incorporated in GROMACS; there have been several recent
extensions of the force field for drug-like molecules that may be useful.

-Justin


Best,

Sencer


On Sun, Feb 5, 2017 at 11:18 AM, Sotirios Dionysios I. Papadatos
 wrote:

automated builders usually produce these mistakes. I see that you already
checked which atoms correspond to this error. Check first if there is an
actual bond there. If it is check ffbonded if these atom types are
parametrized.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 on behalf of Sencer Selcuk

Sent: Wednesday, February 1, 2017 6:18:07 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Propylene Carbonate

Dear all,

I am coming from a first principles background to the classical MD
world, and up until now I used only ReaxFF implementation in LAMMPS
which doesn't really require a topology file of all bonds and angles
etc. Now I would like to do some OPLSaa simulations, starting with
liquid propylene carbonate. That is partly because of a scientific
problem I am interested in, and partly I thought it would be easy to
work with as oplsaa.ff/atomtypes.atp explicitly include the atoms of
propylene carbonate (opls_771 to opls_779).

I tried using topolbuild to generate an initial topology file. It
correctly guessed the correct opls_nnn names most of the atoms. For the
others the atom type (CT, C, O etc.) were correct, and I am providing
charges from literature, so I suppose it wouldn't matter (is that
right?). Still, I changed the opls_nnn names to the correct ones listed
in atomtypes.atp.

My real problem is that one of the angles, OS-C-OS angle, seems to be
missing from the force field files. gmx grompp complains about it (and
about 4 dihedrals, actually) saying:


 ERROR 1 [file molecule.top, line 95]:
   No default Angle types


 ERROR 2 [file molecule.top, line 100]:
   No default Proper Dih. types


 ERROR 3 [file molecule.top, line 101]:
   No default Proper Dih. types


 ERROR 4 [file molecule.top, line 102]:
   No default Proper Dih. types


 ERROR 5 [file molecule.top, line 103]:
   No default Proper Dih. types


I am copying the relevant parts about the missing angle, and the mdp,
gro and top files are attached:



 [atoms]
10opls_773 1PC  OS3  -0.44200  15.99940
;   0.137
11opls_772 1PC   C4   0.85700  12.01100
;   0.994
12opls_771 1PC   O4  -0.51000  15.99940
;   0.484
13opls_773 1PC  OS2  -0.48400  15.99940
;   0.000
 ...
 [angles]
 ...
 101113 ;OS- C-
 OS



I have inspected the ffbonded.itp file manually, and parameters for
OS-C-OS angle is not listed. There is a OS-CO-OS listing, which I
understand belongs to acetal 

Re: [gmx-users] Propylene Carbonate

[Sencer Selcuk]

Justin,

I am pretty sure there is a reliable parametrization of propylene 
carbonate (PC) in OPLSaa. The OPLSaa parameters included in GROMACS 
lists all PC atoms explicitly as well. The opls_771 to opls_779 
non-bonded types correspond to PC atoms.


In the bonded part, however, OS-C-OS angle is missing. I checked the 
parameters provided with Tinker, the same angle is missing.  There are 
several papers & dissertations where people say they used GROMACS and 
the OPLS parameters provided there in to model PC. So I feel like none 
of the parameters are missing, but  I am doing something wrong.


I would really appreciate if you, or someone with experience can take a 
quick look -as I believe this should be a very straight forward example 
of .top generation.


Best,

Sencer


On Mon, Feb 6, 2017 at 7:41 AM, Justin Lemkul  wrote:



On 2/5/17 12:29 PM, Sencer Selcuk wrote:

Sotirios,

Thanks for your response. The angle I am looking at is actually 
present in the
molecule, but the corresponding parameters are missing from the 
ffbonded.itp.
With the hope that white spaces won't be messed when I send this 
email, this is

the propylene carbonate molecule with the bonded atom types listed in
ffnonbonded.itp:

O
||
C
   /  \
OS   OS
 |  |
CT---CT-CT


and the angle I cannot find in the ffbonded.itp is OS-C-OS bond.



If the force field doesn't already have parameters for it, you'll 
need to parametrize it in accordance with the parent force field's 
normal parametrization strategy.  There may be parameters in OPLS-AA 
that are published but not incorporated in GROMACS; there have been 
several recent extensions of the force field for drug-like molecules 
that may be useful.


-Justin


Best,

Sencer


On Sun, Feb 5, 2017 at 11:18 AM, Sotirios Dionysios I. Papadatos
 wrote:
automated builders usually produce these mistakes. I see that you 
already
checked which atoms correspond to this error. Check first if there 
is an
actual bond there. If it is check ffbonded if these atom types are 
parametrized.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 on behalf of 
Sencer Selcuk


Sent: Wednesday, February 1, 2017 6:18:07 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Propylene Carbonate

Dear all,

I am coming from a first principles background to the classical MD
world, and up until now I used only ReaxFF implementation in LAMMPS
which doesn't really require a topology file of all bonds and angles
etc. Now I would like to do some OPLSaa simulations, starting with
liquid propylene carbonate. That is partly because of a scientific
problem I am interested in, and partly I thought it would be easy to
work with as oplsaa.ff/atomtypes.atp explicitly include the atoms of
propylene carbonate (opls_771 to opls_779).

I tried using topolbuild to generate an initial topology file. It
correctly guessed the correct opls_nnn names most of the atoms. For 
the
others the atom type (CT, C, O etc.) were correct, and I am 
providing

charges from literature, so I suppose it wouldn't matter (is that
right?). Still, I changed the opls_nnn names to the correct ones 
listed

in atomtypes.atp.

My real problem is that one of the angles, OS-C-OS angle, seems to 
be
missing from the force field files. gmx grompp complains about it 
(and

about 4 dihedrals, actually) saying:


 ERROR 1 [file molecule.top, line 95]:
   No default Angle types


 ERROR 2 [file molecule.top, line 100]:
   No default Proper Dih. types


 ERROR 3 [file molecule.top, line 101]:
   No default Proper Dih. types


 ERROR 4 [file molecule.top, line 102]:
   No default Proper Dih. types


 ERROR 5 [file molecule.top, line 103]:
   No default Proper Dih. types


I am copying the relevant parts about the missing angle, and the 
mdp,

gro and top files are attached:



 [atoms]
10opls_773 1PC  OS3  -0.44200  15.99940
;   0.137
11opls_772 1PC   C4   0.85700  12.01100
;   0.994
12opls_771 1PC   O4  -0.51000  15.99940
;   0.484
13opls_773 1PC  OS2  -0.48400  15.99940
;   0.000
 ...
 [angles]
 ...
 101113 ;OS- C-
 OS



I have inspected the ffbonded.itp file manually, and parameters for
OS-C-OS angle is not listed. There is a OS-CO-OS listing, which I
understand belongs to acetal like structures. Shall I use this -as I
have seen numerous literature examples where people say "we used 
OPLSaa

force field" to describe propylene carbonate, without giving any
details. I am pretty sure, the problem is not about the force field
file itself, it is not missing a line or anything like that - I also
looked at the oplsaa parameteres of Tinker, and parameters for the 
same

angle is missing 

[gmx-users] Force field for Cobalt topology??

[Amir Zeb]

Hello gmx users,

I'm wondering which would be the best force field to create topology for
cobalt. I tried different ff but none of them get the task. I searched the
mailing archive too but I couldn't get the way to solve the issue.
Dr. Justin has just mentioned (https://www.mail-archive.com/gmx
us...@gromacs.org/msg46374.html) that there is no such suitable force field
yet to deal with transition metals correctly due to their lack of fixed
charge. But this was commented so back.
Let me know if the recent advances had solved such issue.

Regards!

Amir
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Re: [gmx-users] Why the individual interaction potentials are additive?

[Mark Abraham]

Hi,

Simply that it makes a useful physical model. If one has a gravitational
system with one body, then there's a single term in the potential; with
two, there's two terms added, etc. Electrostatics work the same way, of
course. Bonded interactions are a practical hack that recognize that
multi-body and non-nuclear effects are strong at very short range. So one
excludes the "normal" non-bonded interactions, and replaces their
contribution with whatever functional form + parameters seem to work well.
The additivity is simply intrinsic to the model. You can't multiply the
non-bonded interaction potential by the bonded one and get something
sensible :-)

Mark

On Mon, Feb 6, 2017 at 2:31 PM ibrahim khalil 
wrote:

> Dear GROMACS users,
>
> I had a somewhat of a basic (or elementary) question.
>
> While doing MD simulations, we use interaction potentials that consist of
> bonded and nonbonded potential terms- then again the bonded term consists
> of some other potential terms such as bond, angle, dihedral etc.
>
> My question is-*Why the terms are additive?*
>
> Inside this book of R. LeSar, Introduction to Computational Materials
> Science, 2013, I found- the potential energy of a system can be expanded as
> a series of terms involving pair, triplets and quadriples of atoms etc. and
> we ignore the rest of the higher interaction terms.
>
> -which might explain the bonded interactions being additve.
>
> But why the nonbonded interactions are additive to the bonded ones?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] gromacs installing problems with "cmake .."

[Mark Abraham]

Hi,

You need a C++ compiler on your system, e.g.
http://askubuntu.com/questions/689722/how-to-install-a-c-c-compiler-in-ubuntu-14-04lts

Mark

On Mon, 6 Feb 2017 14:12 Zhang, Cheng  wrote:

Dear Gromacs users,

I got a list of errors after running "cmake ..". I am sure the "cmake"
itself is already installed. I am installing Gromacs 5.1.4 on
ubuntu-14.04.1 on VMwarePlayer on a Dell PC. Can I ask how to solve this?


Thank you.

Yours sincerely

Cheng


ucbepan@ubuntu:/mnt/hgfs/Documents/gromacs-5.1.4/build$ cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-- The CXX compiler identification is unknown
CMake Error: your CXX compiler: "CMAKE_CXX_COMPILER-NOTFOUND" was not
found.   Please set CMAKE_CXX_COMPILER to a valid compiler path or name.
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU
acceleration
CMake Warning at cmake/gmxTestCompilerProblems.cmake:41 (message):
  The ids of the C and C++ compilers do not match (GNU and , respectively).
  Mixing different C/C++ compilers can cause problems.
Call Stack (most recent call first):
  CMakeLists.txt:310 (gmx_test_compiler_problems)


CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message):
  The versions of the C and C++ compilers do not match (4.8.2 and ,
  respectively).  Mixing different C/C++ compilers can cause problems.
Call Stack (most recent call first):
  CMakeLists.txt:310 (gmx_test_compiler_problems)


CMake Error at cmake/gmxManageSimd.cmake:67 (message):
  Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1
SIMD
  (slower).
Call Stack (most recent call first):
  cmake/gmxManageSimd.cmake:261
(gmx_give_fatal_error_when_simd_support_not_found)
  CMakeLists.txt:648 (gmx_manage_simd)


-- Configuring incomplete, errors occurred!
See also
"/mnt/hgfs/Documents/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log".
See also
"/mnt/hgfs/Documents/gromacs-5.1.4/build/CMakeFiles/CMakeError.log".
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[gmx-users] Why the individual interaction potentials are additive?

[ibrahim khalil]

Dear GROMACS users,

I had a somewhat of a basic (or elementary) question.

While doing MD simulations, we use interaction potentials that consist of
bonded and nonbonded potential terms- then again the bonded term consists
of some other potential terms such as bond, angle, dihedral etc.

My question is-*Why the terms are additive?*

Inside this book of R. LeSar, Introduction to Computational Materials
Science, 2013, I found- the potential energy of a system can be expanded as
a series of terms involving pair, triplets and quadriples of atoms etc. and
we ignore the rest of the higher interaction terms.

-which might explain the bonded interactions being additve.

But why the nonbonded interactions are additive to the bonded ones?
-- 
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[gmx-users] gromacs installing problems with "cmake .."

[Zhang, Cheng]

Dear Gromacs users,

I got a list of errors after running "cmake ..". I am sure the "cmake" itself 
is already installed. I am installing Gromacs 5.1.4 on ubuntu-14.04.1 on 
VMwarePlayer on a Dell PC. Can I ask how to solve this?


Thank you.

Yours sincerely

Cheng


ucbepan@ubuntu:/mnt/hgfs/Documents/gromacs-5.1.4/build$ cmake .. 
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-- The CXX compiler identification is unknown
CMake Error: your CXX compiler: "CMAKE_CXX_COMPILER-NOTFOUND" was not found.   
Please set CMAKE_CXX_COMPILER to a valid compiler path or name.
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration
CMake Warning at cmake/gmxTestCompilerProblems.cmake:41 (message):
  The ids of the C and C++ compilers do not match (GNU and , respectively).
  Mixing different C/C++ compilers can cause problems.
Call Stack (most recent call first):
  CMakeLists.txt:310 (gmx_test_compiler_problems)


CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message):
  The versions of the C and C++ compilers do not match (4.8.2 and ,
  respectively).  Mixing different C/C++ compilers can cause problems.
Call Stack (most recent call first):
  CMakeLists.txt:310 (gmx_test_compiler_problems)


CMake Error at cmake/gmxManageSimd.cmake:67 (message):
  Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1 SIMD
  (slower).
Call Stack (most recent call first):
  cmake/gmxManageSimd.cmake:261 
(gmx_give_fatal_error_when_simd_support_not_found)
  CMakeLists.txt:648 (gmx_manage_simd)


-- Configuring incomplete, errors occurred!
See also "/mnt/hgfs/Documents/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log".
See also "/mnt/hgfs/Documents/gromacs-5.1.4/build/CMakeFiles/CMakeError.log".
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[gmx-users] OPLS-AA forcefield for perfluoroalkanes

[Pedro Morgado]

Dear all,

I am currently simulating perfluoroalkanes with gromacs, and I have
detected that the parameters for the F-C-C-F dihedral in the opls-aa
parameter file (ffbonded.itp) do not match the parameters published in the
original Watkins and Jorgensen paper (J. Phys. Chem. A 2001, 105 (16),
4118–4125.).
In more detail, the parameter file has the RB coefficients: [-5.23 5.23 0.0
0.0 0.0 0.0], instead of [-4.707 6.799 0.0 -2.092 0.0 0.0], which result
from the conversion of the parameters in Watkins' paper from Fourier to RB
form and from kCal to kJ.

Does anyone know if there is a reason for this difference (perhaps a typo
in the published paper)? Or if this is just an error in the parameter file?

Thank you,
Pedro Morgado
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Re: [gmx-users] How to connect ligating residues ??

[Justin Lemkul]

On 2/6/17 12:13 AM, Mehreen Jan wrote:

Hello,
 Hope so you are doing well. Thanks a lot for your kind response.
Version : 5.0.7
FF: 43a1 Spc water model.

Your Suggestion:
"You should not need external servers to generate a heme topology; GROMOS 
already
supports it.  It's called HEME and it's in the .rtp file.  Connections to
ligating residues should be recognized via existing entries in specbond.dat."

This oxygen molecule is attached as a ligand to heme.
HETATM 1  O1  OXY C1543   5.525  80.353  -6.212  1.00 25.38  O
HETATM 2  O2  OXY C1543   4.301  80.342  -6.721  1.00 30.35  O
END

Now my question is how connections to ligating residues should be recognized 
via existing entries in specbond.dat.

The specbond.dat file contains the following:
8
CYS SG  1   CYS SG  1   0.2 CYS2CYS2
CYS SG  1   HEM FE  2   0.25CYS2HEME
CYS SG  1   HEM CAB 1   0.18CYS2HEME
CYS SG  1   HEM CAC 1   0.18CYS2HEME
HIS NE2 1   HEM FE  1   0.2 HIS1HEME
MET SD  1   HEM FE  1   0.24MET HEME
CO  C   1   HEMEFE  1   0.19CO  HEME
CYM  SG  1   CYM SG  1   0.2 CYS2CYS2

Waiting for your kind response. I shall be very thankful to you.


Please read manual section 5.7.7.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] Block Copolymer

[Justin Lemkul]

On 2/5/17 11:29 PM, NIKHIL JOSHI wrote:

hi

I want to simulate block copolymer Polyethylene- Polyethylene oxide
(PE-PEO).
I have the individual results of PE and PEO. My question is how to connect
this two polymers and simulate? what is the procedure to make block
copolymer?



http://www.gromacs.org/Documentation/How-tos/Polymers

-Justin

--
==

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

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

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

==
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Re: [gmx-users] Propylene Carbonate

[Justin Lemkul]

On 2/5/17 12:29 PM, Sencer Selcuk wrote:

Sotirios,

Thanks for your response. The angle I am looking at is actually present in the
molecule, but the corresponding parameters are missing from the ffbonded.itp.
With the hope that white spaces won't be messed when I send this email, this is
the propylene carbonate molecule with the bonded atom types listed in
ffnonbonded.itp:

O
||
C
   /  \
OS   OS
 |  |
CT---CT-CT


and the angle I cannot find in the ffbonded.itp is OS-C-OS bond.



If the force field doesn't already have parameters for it, you'll need to 
parametrize it in accordance with the parent force field's normal 
parametrization strategy.  There may be parameters in OPLS-AA that are published 
but not incorporated in GROMACS; there have been several recent extensions of 
the force field for drug-like molecules that may be useful.


-Justin


Best,

Sencer


On Sun, Feb 5, 2017 at 11:18 AM, Sotirios Dionysios I. Papadatos
 wrote:

automated builders usually produce these mistakes. I see that you already
checked which atoms correspond to this error. Check first if there is an
actual bond there. If it is check ffbonded if these atom types are parametrized.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 on behalf of Sencer Selcuk

Sent: Wednesday, February 1, 2017 6:18:07 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Propylene Carbonate

Dear all,

I am coming from a first principles background to the classical MD
world, and up until now I used only ReaxFF implementation in LAMMPS
which doesn't really require a topology file of all bonds and angles
etc. Now I would like to do some OPLSaa simulations, starting with
liquid propylene carbonate. That is partly because of a scientific
problem I am interested in, and partly I thought it would be easy to
work with as oplsaa.ff/atomtypes.atp explicitly include the atoms of
propylene carbonate (opls_771 to opls_779).

I tried using topolbuild to generate an initial topology file. It
correctly guessed the correct opls_nnn names most of the atoms. For the
others the atom type (CT, C, O etc.) were correct, and I am providing
charges from literature, so I suppose it wouldn't matter (is that
right?). Still, I changed the opls_nnn names to the correct ones listed
in atomtypes.atp.

My real problem is that one of the angles, OS-C-OS angle, seems to be
missing from the force field files. gmx grompp complains about it (and
about 4 dihedrals, actually) saying:


 ERROR 1 [file molecule.top, line 95]:
   No default Angle types


 ERROR 2 [file molecule.top, line 100]:
   No default Proper Dih. types


 ERROR 3 [file molecule.top, line 101]:
   No default Proper Dih. types


 ERROR 4 [file molecule.top, line 102]:
   No default Proper Dih. types


 ERROR 5 [file molecule.top, line 103]:
   No default Proper Dih. types


I am copying the relevant parts about the missing angle, and the mdp,
gro and top files are attached:



 [atoms]
10opls_773 1PC  OS3  -0.44200  15.99940
;   0.137
11opls_772 1PC   C4   0.85700  12.01100
;   0.994
12opls_771 1PC   O4  -0.51000  15.99940
;   0.484
13opls_773 1PC  OS2  -0.48400  15.99940
;   0.000
 ...
 [angles]
 ...
 101113 ;OS- C-
 OS



I have inspected the ffbonded.itp file manually, and parameters for
OS-C-OS angle is not listed. There is a OS-CO-OS listing, which I
understand belongs to acetal like structures. Shall I use this -as I
have seen numerous literature examples where people say "we used OPLSaa
force field" to describe propylene carbonate, without giving any
details. I am pretty sure, the problem is not about the force field
file itself, it is not missing a line or anything like that - I also
looked at the oplsaa parameteres of Tinker, and parameters for the same
angle is missing in that case as well. Then what do I do with the
missing dihedrals (it is the whole first dihedrals section in the .top
file)?

Finally, the .top file generated by topolbuild has other lines with
"missing" data, as well. But I can find the relevant parameters in the
ffbonded.itp file, and grompp does not complain anyway. So can I
suppose it is going to use the correct parameters for these lines?



  7 5 61 110.700313.8000 ;CT-CT-
  HC
  7 513   1 109.500418.4000 ;CT-CT-
 OS
  5   1311  ;
   CT-OS- C ;  data missing
  5 710   1 109.500418.4000 ;CT-CT-
 OS
  5 7 81 110.700313.8000 ;CT-CT-
  HC
  5 7 91 110.700313.8000 ;CT-CT-
  HC


I really 

Re: [gmx-users] INDEX

[Erik Marklund]

Dear Subashini,

You forgot to provide trjconv with the index file you created. Try gmx trjconv 
-n your_index_file.ndx …

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se

On 6 Feb 2017, at 13:06, Subashini .K 
> wrote:

Hi gromacs users,


I want to visualize the results of simulations using the command


gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb


Wish to see Protein and ligand simulations together in the pdb file.


But, when the command is given, we can either select protein group or ligand 
group


Before this was done,


The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt


However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in 
the movie.pdb file.


What to do?

Can someone help?


Thanks,

Subashini.K


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[gmx-users] INDEX

[Subashini .K]

Hi gromacs users,


I want to visualize the results of simulations using the command


gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb


Wish to see Protein and ligand simulations together in the pdb file.


But, when the command is given, we can either select protein group or ligand 
group


Before this was done,


The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt


However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in 
the movie.pdb file.


What to do?

Can someone help?


Thanks,

Subashini.K


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Re: [gmx-users] Periodicity in x-y plane (Neda Rafiee)

[Björn Sommer]

Hi Neda,

On 6/02/2017 8:43 am, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
wrote:
>6. Periodicity in x-y plane (Neda Rafiee)
>
>
>
> Message: 6
> Date: Mon, 6 Feb 2017 11:08:42 +0330 (IRST)
> From: Neda Rafiee 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Periodicity in x-y plane
> Message-ID: <12473704.8815.1486366722721.javamail.r...@zmail.ipm.ir>
> Content-Type: text/plain; charset=utf-8
>
> Hi. I have already built a lipid bilayer and I want to create a box for it 
> and fill it with water. I used : 
> $ gmx editconf -f renumber.gro -o newbox.gro  -c -box 8 8 14 -bt triclinic  
> and after that I used:
> $ gmx solvate -cp newbox.gro -cs tip4p.gro -o solvated.gro -p topol.top  
>
> but when I see solvated.gro in VMD, in periodicity , I check x +x or y +y 
> direction, I see man water molecules between adjacent neighbors in x-y 
> direction and it destroy the periodicity of my membrane in x-y plane, while I 
> want to have water only in the upper and lower sides of the membrane. What 
> should I do? 
>
>
Please play around with this:
http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=21=641

Shortly, in VMD use in the Graphical Representations window a selection like
not ((resname 'W' 'NA+') and within 5.5 of (not resname 'W' 'NA+'))

See the previous link for more info. Basically, make sure that no water
is inside the membrane but also that the distance between the water bath
and the head groups is not too small, otherwise the box will shrink
during simulation and the membrane might deform a little bit.

After that, use the regular PDB export and make sure to select the
actual selection in the export window!/
/
Have fun!
Bjorn
/
/
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Re: [gmx-users] MD simulation of peptide amphiphile using CG method

[Graham J . A .]

You can take the standard parameters for the amino acid and hydrocarbon
components, but as you said, the difficulty is in the link.  You'll need
to find an existing MARTINI molecule with a similar link in it and take
the parameters from that.  If there isn't an existing molecule you can
copy from then the easiest way to get the new parameters is from
atomistic simulation.

It's also important to validate any new CG model which can be done
either against experimental data, or again against atomistic simulation
(ideally both).

Martinize.py will only be able to convert an atomistic structure if the
molecule has been defined in its database, it won't work on a new
molecule until you tell it the parameters to use.  It's obviously
recognising the protein component and giving you parameters for that,
but doesn't know what to do about the hydrocarbon tail.

Yes, the easiest thing to do would be to copy a residue from the amino
acids itp and modify it there, but you'll still need to get the
parameters of the bond to the hydrocarbon tail.

James


On Fri, 2017-02-03 at 18:53 +0330, leila karami wrote:
> Dear James,
> 
> Thanks for your answer.
> 
> As I understand, PyCGTOOL generates the coarse-grained molecular dynamics
> models from atomistic simulation trajectories. But, I don't want to do
> the atomistic simulation.
> 
> Also, ATB only generates a complete topology for molecules containing < 40
> atoms, while I have 5 PA molecules with > 40 atoms, apiece.
> 
> Since my molecules contain amino acids bonded to the hydrocarbon chain
> (which are default beads in Martini force field), I think there is
> a straightforward way for treatment of that. Unfortunately, I don't have
> experience about that. My problem is how to relate amino acids to hydrocarbon
> chain?
> 
> When I use martinize.py, in structure and topology output files, there are
> only amino acids and not hydrocarbon chain.
> 
> Should I modify martini_v2.2_aminoacids.itp by adding hydrocarbon tail
> parameter to it?
> 
> Best,
> LK

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Re: [gmx-users] Membrane cutt-offs

[Neda Rafiee]

Thanks Catarina!

Kind regards,
Neda Rafieiolhosseini
Ph.D. Student at Institute for Research
in Fundamental Sciences(IPM),
School of Nano,
Tehran,Iran. 

- Original Message -
From: "Catarina A. Carvalheda dos Santos" 
To: "Discussion list for GROMACS users" 
Sent: Monday, February 6, 2017 1:55:27 PM
Subject: Re: [gmx-users] Membrane cutt-offs

Hi,

Just check the paper corresponding to the lipid force field you want to use.

Cheers,

On 6 February 2017 at 06:41, Neda Rafiee  wrote:

> Hi!
> I have a question regarding to cut-off values for membranes. I know that
> using usual cut-offs is not appropriate for systems including membrane.
> Where can I find the appropriate values?
>
>
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>
> 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
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Re: [gmx-users] Membrane cutt-offs

[Catarina A. Carvalheda dos Santos]

Hi,

Just check the paper corresponding to the lipid force field you want to use.

Cheers,

On 6 February 2017 at 06:41, Neda Rafiee  wrote:

> Hi!
> I have a question regarding to cut-off values for membranes. I know that
> using usual cut-offs is not appropriate for systems including membrane.
> Where can I find the appropriate values?
>
>
> --
> Gromacs Users mailing list
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> 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
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Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

[Kroon, P.C.]

Hi,

I don't have an example at hand, but I'll remember!
Thanks for the hard work :)

Peter

On Mon, Feb 6, 2017 at 10:08 AM, Mark Abraham 
wrote:

> Hi,
>
> If so, please share a case on https://redmine.gromacs.org that doesn't
> work
> as you think it should. We're very happy to make things work better!
>
> Mark
>
> On Mon, 6 Feb 2017 10:04 Kroon, P.C.  wrote:
>
> > Alternatively, center it on an interfacial residue. pbc cluster doesn't
> > always work, unfortunately.
> >
> > Peter
> >
> > On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
> > chris.ne...@alum.utoronto.ca> wrote:
> >
> > > Awesome Mark, thanks! It works.
> > >
> > > I filed a bug about a nonexistent -clustercenter option mentioned in
> the
> > > v5.1.2 help file, but the command seems to work anyway for my usage.
> > >
> > > Thanks again,
> > > Chris.
> > > 
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > > Abraham 
> > > Sent: 04 February 2017 07:27:52
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] how to reimage PBC based on distance to a
> given
> > > selection without recentering or otherwise changing atomic coordinates
> > >
> > > Hi,
> > >
> > > I've never really use it myself, but I imagine trjconv -pbc cluster is
> > > useful for this kind of scenario when you want to treat a group of
> > > molecules as indivisible.
> > >
> > > Mark
> > >
> > > On Sat, 4 Feb 2017 09:33 Christopher Neale <
> chris.ne...@alum.utoronto.ca
> > >
> > > wrote:
> > >
> > > > Dear users:
> > > >
> > > > I have a system in which molecule A is in direct contact with
> molecule
> > B.
> > > > However, molecule B is imaged in a different periodic cell. What I
> > would
> > > > like to do is to get an image of both molecules in a periodic
> > > > representation in which they actually are in contact (i.e., reimage
> > > > molecule B such that it is closest to molecule A). However, I do not
> > want
> > > > to lose spatial information with e.g. a trjconv -center -pbc mol
> > command.
> > > >
> > > > This is part of a complex automated build procedure and I can get
> into
> > > > more details if that is useful, but the crux is that I am extracting
> a
> > > > frame from a simulation, building more atoms onto molecule A, and
> > setting
> > > > up a new simulation. To build onto molecule A, I want to then do a
> > vacuum
> > > > EM before adding it back to the water box, for which I first enlarge
> > the
> > > > vacuum box, and changing box dimensions is messing with the
> periodicity
> > > and
> > > > throwing molecule B away from molecule A in an unrealistic fashion
> > > > (molecule B is a tightly bound ligand).
> > > >
> > > > I could do what I want by breaking each molecule out into its own
> box,
> > > > checking for contacts, reimaging, and then putting them back
> together.
> > I
> > > > presume (but have not checked) that I could also do this by making a
> > new
> > > > .itp file in which both molecule A and B are part of the same [
> > molecule
> > > ]
> > > > definition and then running a zero-step mdrun. However, I am writing
> to
> > > see
> > > > if anybody knows how reimage based on a selection (would be a single
> > atom
> > > > in molecule A near the contact between molecule A and B) more
> elegantly
> > > > with processing tools available in gromacs.
> > > >
> > > > Thank you for your help,
> > > > Chris.
> > > > --
> > > > 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
> > >
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Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

[Mark Abraham]

Hi,

If so, please share a case on https://redmine.gromacs.org that doesn't work
as you think it should. We're very happy to make things work better!

Mark

On Mon, 6 Feb 2017 10:04 Kroon, P.C.  wrote:

> Alternatively, center it on an interfacial residue. pbc cluster doesn't
> always work, unfortunately.
>
> Peter
>
> On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
> chris.ne...@alum.utoronto.ca> wrote:
>
> > Awesome Mark, thanks! It works.
> >
> > I filed a bug about a nonexistent -clustercenter option mentioned in the
> > v5.1.2 help file, but the command seems to work anyway for my usage.
> >
> > Thanks again,
> > Chris.
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > Abraham 
> > Sent: 04 February 2017 07:27:52
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] how to reimage PBC based on distance to a given
> > selection without recentering or otherwise changing atomic coordinates
> >
> > Hi,
> >
> > I've never really use it myself, but I imagine trjconv -pbc cluster is
> > useful for this kind of scenario when you want to treat a group of
> > molecules as indivisible.
> >
> > Mark
> >
> > On Sat, 4 Feb 2017 09:33 Christopher Neale  >
> > wrote:
> >
> > > Dear users:
> > >
> > > I have a system in which molecule A is in direct contact with molecule
> B.
> > > However, molecule B is imaged in a different periodic cell. What I
> would
> > > like to do is to get an image of both molecules in a periodic
> > > representation in which they actually are in contact (i.e., reimage
> > > molecule B such that it is closest to molecule A). However, I do not
> want
> > > to lose spatial information with e.g. a trjconv -center -pbc mol
> command.
> > >
> > > This is part of a complex automated build procedure and I can get into
> > > more details if that is useful, but the crux is that I am extracting a
> > > frame from a simulation, building more atoms onto molecule A, and
> setting
> > > up a new simulation. To build onto molecule A, I want to then do a
> vacuum
> > > EM before adding it back to the water box, for which I first enlarge
> the
> > > vacuum box, and changing box dimensions is messing with the periodicity
> > and
> > > throwing molecule B away from molecule A in an unrealistic fashion
> > > (molecule B is a tightly bound ligand).
> > >
> > > I could do what I want by breaking each molecule out into its own box,
> > > checking for contacts, reimaging, and then putting them back together.
> I
> > > presume (but have not checked) that I could also do this by making a
> new
> > > .itp file in which both molecule A and B are part of the same [
> molecule
> > ]
> > > definition and then running a zero-step mdrun. However, I am writing to
> > see
> > > if anybody knows how reimage based on a selection (would be a single
> atom
> > > in molecule A near the contact between molecule A and B) more elegantly
> > > with processing tools available in gromacs.
> > >
> > > Thank you for your help,
> > > Chris.
> > > --
> > > 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
> >
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Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

[Kroon, P.C.]

Alternatively, center it on an interfacial residue. pbc cluster doesn't
always work, unfortunately.

Peter

On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Awesome Mark, thanks! It works.
>
> I filed a bug about a nonexistent -clustercenter option mentioned in the
> v5.1.2 help file, but the command seems to work anyway for my usage.
>
> Thanks again,
> Chris.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 04 February 2017 07:27:52
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] how to reimage PBC based on distance to a given
> selection without recentering or otherwise changing atomic coordinates
>
> Hi,
>
> I've never really use it myself, but I imagine trjconv -pbc cluster is
> useful for this kind of scenario when you want to treat a group of
> molecules as indivisible.
>
> Mark
>
> On Sat, 4 Feb 2017 09:33 Christopher Neale 
> wrote:
>
> > Dear users:
> >
> > I have a system in which molecule A is in direct contact with molecule B.
> > However, molecule B is imaged in a different periodic cell. What I would
> > like to do is to get an image of both molecules in a periodic
> > representation in which they actually are in contact (i.e., reimage
> > molecule B such that it is closest to molecule A). However, I do not want
> > to lose spatial information with e.g. a trjconv -center -pbc mol command.
> >
> > This is part of a complex automated build procedure and I can get into
> > more details if that is useful, but the crux is that I am extracting a
> > frame from a simulation, building more atoms onto molecule A, and setting
> > up a new simulation. To build onto molecule A, I want to then do a vacuum
> > EM before adding it back to the water box, for which I first enlarge the
> > vacuum box, and changing box dimensions is messing with the periodicity
> and
> > throwing molecule B away from molecule A in an unrealistic fashion
> > (molecule B is a tightly bound ligand).
> >
> > I could do what I want by breaking each molecule out into its own box,
> > checking for contacts, reimaging, and then putting them back together. I
> > presume (but have not checked) that I could also do this by making a new
> > .itp file in which both molecule A and B are part of the same [ molecule
> ]
> > definition and then running a zero-step mdrun. However, I am writing to
> see
> > if anybody knows how reimage based on a selection (would be a single atom
> > in molecule A near the contact between molecule A and B) more elegantly
> > with processing tools available in gromacs.
> >
> > Thank you for your help,
> > Chris.
> > --
> > 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!
>
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