[gmx-users] Angle group

Cyrus Djahedi cyrusdja at kth.se
Thu Jul 24 14:55:30 CEST 2014 

I tried using g_angle with an index file defining the three atoms that make up the bond as "Group    12 (       O1_C1_C4) has   960 elements". I get:

Group     0 (         System) has 27396 elements
Group     1 (          Other) has  6768 elements
Group     2 (           GL4b) has   352 elements
Group     3 (           G14b) has  6048 elements
Group     4 (           GL1b) has   368 elements
Group     5 (          Water) has 20628 elements
Group     6 (            SOL) has 20628 elements
Group     7 (      non-Water) has  6768 elements
Group     8 (             O1) has   320 elements
Group     9 (             O4) has    16 elements
Group    10 (             C1) has   320 elements
Group    11 (             C4) has   320 elements
Group    12 (       O1_C1_C4) has   960 elements
Group    13 (       C1_O1_C4) has   960 elements
Group    14 (       C4_C1_O1) has   960 elements
Group    15 (       C1_C4_O1) has   960 elements
Group    16 (       O1_C1_C4) has   960 elements
Select a group: 12
Selected 12: 'O1_C1_C4'
Last frame      10000 time 10000.000   
Found points in the range from 5 to 43 (max 180)
 < angle >  = 23.1856
< angle^2 > = 537.601
Std. Dev.   = 0.170041

I dont know exactly what angle it is referring to. The angle I'm looking for is formed at the O1-atom, flanked by the carbon atoms and is around 118-120 degrees . As you can see in the index-options I tried defining the triplets in different order, this made no difference however. Any suggestions?

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Today's Topics:

   1. Re: Diffusion coefficient of metal complex (Justin Lemkul)
   2. Re: Angle group (Justin Lemkul)
   3. Re: Error in system_inflate.gro coordinates does not      match
      (RINU KHATTRI)
   4. coulomb interactions with zero charge atoms (Sikandar Mashayak)
   5. Re: Error in system_inflate.gro coordinates does not match
      (Justin Lemkul)
   6. Lennard-Jones potential not matching with published data
      (ibrahim khalil)


----------------------------------------------------------------------

Message: 1
Date: Wed, 23 Jul 2014 07:31:13 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Diffusion coefficient of metal complex
Message-ID: <53CF9D01.60206 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 7/23/14, 7:13 AM, Meena Singh wrote:
> Dear GROMACS users,
>
> I'm working on the diffusivity of metal ion with its ligand in organic
> phase.
>
> I want to calculate the diffusion coefficient of metal-ligand complex as a
> group, but when I run g_msd command the option are there for only
> individual molecules diffusivity calculation.
>
> Can I calculate the diffusion coefficient of specific complex from the box
> which contains metal ions and ligand molecules.
>
> Does anyone have a suggestion to help me with this problem?
>

Create an index group for whatever subset of atoms you like and use it for the
calculation.

-Justin

--
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================


------------------------------

Message: 2
Date: Wed, 23 Jul 2014 07:30:55 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org, vvchaban at gmail.com
Subject: Re: [gmx-users] Angle group
Message-ID: <53CF9CEF.3070001 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 7/23/14, 5:58 AM, Dr. Vitaly Chaban wrote:
> Use g_angle and your index file must contain triples of the involved atoms.
>
> if I remember correctly, this route provides a gaussian-type
> probability distribution, i.e. not evolution vs. time.
>

The default behavior is to produce a distribution, but g_angle -ov -all will
produce individual time series of all the angles in the chosen index group.

-Justin

--
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================


------------------------------

Message: 3
Date: Wed, 23 Jul 2014 21:42:07 +0530
From: RINU KHATTRI <nickname.mittu at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does
        not     match
Message-ID:
        <CAOEfx3KudSa2Mj74guRB9VB_oEQu3nZ73YQEkzN4eOLiE8Cs=g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

hello everyone
thank you justin but how can i increase the box size i am using the box
vector which is present in popc_whole.gro
how can i edit it
and one more problem when i see it in vmd my ligand is out side the protein
kindly help



On Wed, Jul 23, 2014 at 5:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/23/14, 12:48 AM, RINU KHATTRI wrote:
>
>> hello everyone
>>
>> ok justin iam sending you the link of images
>> http://s48.photobucket.com/user/mittukhattri/media/
>> Screenshot-3_zps81b0c070.png.html
>> http://i48.photobucket.com/albums/f213/mittukhattri/
>> Screenshot-3_zps81b0c070.png
>>
>
> Rendering the box vectors would be helpful, but my guess is your box is
> too small along z, so your protein jumps between periodic images, giving
> the impression that it is "outside" the membrane.
>
> -Justin
>
>
>  ; Include Position restraint file
>> #ifdef  POSRES
>> #include "posre.itp"
>> #endif
>> ; Strong position restraints for InflateGRO
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>> ; Strong position restraints for InflateGRO
>> #ifdef STRONG_POSRES
>> #include "backbone_posre.itp"
>> #endif
>> ; Include ligand topology
>> #include "drag.itp"
>>
>> ; Ligand position restraints
>> #ifdef   DPOSRES_LIG
>> #include "posre_UNK.itp"
>> #endif
>>
>> ; Include POPC chain topology
>> #include "popc.itp"
>>
>> ; Include water topology
>> #include "gromos53a6_lipid.ff/spc.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx          fcy         fcz
>>     1    1        1000000    1000000    1000000
>>     2    2       1000000    1000000    1000000
>>     3     3       1000000    1000000    1000000
>> #endif
>>
>> ; Include topology for ions
>> #include "gromos53a6.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Displayed atoms in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> UNK                 1
>> POPC               122
>> this is my topology
>> i will  add water and ions after the shrinking step
>>   i did't get inflategro2.pl script i used infltegro.pl
>> kindly help
>>
>>
>> On Tue, Jul 22, 2014 at 4:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/21/14, 11:30 AM, RINU KHATTRI wrote:
>>>
>>>  hello everyone
>>>>
>>>> thanks justin it works but problem is at the same place even one more
>>>> problem ligand is out side the protein and protein is out side the popc
>>>>
>>>>
>>> So you've placed the ligand incorrectly or otherwise manipulated the
>>> coordinates wrong.  Given the absence of any other information, it's
>>> impossible to suggest anything.
>>>
>>> -Justin
>>>
>>>
>>>   kindly help
>>>
>>>>
>>>>
>>>> On Sat, Jul 19, 2014 at 7:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 7/19/14, 9:56 AM, RINU KHATTRI wrote:
>>>>>
>>>>>   hello everyone
>>>>>
>>>>>>
>>>>>> i know justin -D is for minim.mdp not for topology i used simply D
>>>>>>
>>>>>>
>>>>>>  That's still wrong.  There should be no "D" or "-D" in the #ifdef
>>>>> statement; it's cpp macro syntax.  Please look at the block I provided
>>>>> before:
>>>>>
>>>>>
>>>>> #ifdef STRONG_POSRES
>>>>> #include "strong_posre.itp"
>>>>> #endif
>>>>>
>>>>> Use it exactly.  Copy and paste it.  Invoke it with "define =
>>>>> -DSTRONG_POSRES"
>>>>>
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 601
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at 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-request at gromacs.org.
>>>>>
>>>>>
>>>>>  --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at 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-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at 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-request at gromacs.org.
>


------------------------------

Message: 4
Date: Wed, 23 Jul 2014 09:42:10 -0700
From: Sikandar Mashayak <symashayak at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: [gmx-users] coulomb interactions with zero charge atoms
Message-ID:
        <CAH+j+HJ+ah4aicPp4svOYFzKy0LsR4JMVm6sGjLHk62PDNgr+g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi

I am wondering if I have a system of simple LJ atoms with no charge on
then, will gromacs still compute coulomb interaction computations?

Thanks,
Sikandar


------------------------------

Message: 5
Date: Wed, 23 Jul 2014 13:18:57 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does
        not match
Message-ID: <53CFEE81.5090809 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 7/23/14, 12:12 PM, RINU KHATTRI wrote:
> hello everyone
> thank you justin but how can i increase the box size i am using the box
> vector which is present in popc_whole.gro
> how can i edit it

editconf

> and one more problem when i see it in vmd my ligand is out side the protein

Position the protein-ligand complex like you want before packing the lipids
around the protein, remove the ligand, then assemble the membrane protein
system.  With strong restraints, the protein should not move, so you can just
paste in the ligand coordinates afterwards.  Then adjust the box and solvate.

-Justin

--
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================


------------------------------

Message: 6
Date: Thu, 24 Jul 2014 00:40:14 +0600
From: ibrahim khalil <ibrahim.khalil.chem at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Lennard-Jones potential not matching with
        published data
Message-ID:
        <CAPUjB3Vx7R7xyZ85O0ywxWEu=J2u+uMbhrC44M3OBa45nXNDEQ at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear gromacs users, i know this is not a good question to post here but i
am trying to reproduce some published data where the Lennard-Jones
potential is plotted with respect to time.

In my simulation, my results are about half (not exactly half but around
half) of the published data. I am stuck here for like a month and cannot
find my mistakes.

Can anyone help me where to look for my mistake? I am using a modified
oplsaa forcefield.

Should i check my forcefield parameters? Or my mdp parameters?


------------------------------

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