[gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 165
Biplab Ghosh
ghosh.biplab at gmail.com
Wed May 27 06:53:03 CEST 2015
Thank you Justin.
I am sorry for not being able to properly pose the problem!
I need to know the variation in distance between two residues during the
course of the trajectory. I was not sure whether the command was correct
or not!
Regards,
--BG
On 27 May 2015 at 02:22, <gromacs.org_gmx-users-request at maillist.sys.kth.se>
wrote:
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> Today's Topics:
>
> 1. Re: Variation of distance between 2 CA atoms with time
> (Justin Lemkul)
> 2. Re: #include section in a .top file (Justin Lemkul)
> 3. Re: trjconv command not found (Justin Lemkul)
> 4. Re: Index file (Justin Lemkul)
> 5. Re: Molecule specific explosion (Eric Smoll)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 26 May 2015 16:46:49 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Variation of distance between 2 CA atoms with
> time
> Message-ID: <5564DBB9.8020405 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/26/15 8:42 AM, Biplab Ghosh wrote:
> > Dear Gromacs Users,
> >
> > I am new to Gromacs and using Gromacs-5.0.4.
> >
> > I want to calculate the variation of distance between to
> > C-alpha atoms in a protein in course of time.
> >
> > First, I have created a file called: L153_V161.ndx using make_ndx
> > and the content of the file is:
> >
> > [ L153 ]
> > 2277
> > [ V161 ]
> > 2394
> >
> > Then I was running the following command:
> >
> > gmx_mpi distance -f protein.xtc -s protein.gro -n L153_V161.ndx -select
> > 'com of group "L153" plus com of group "V161"' -oav
> >
> > I am not getting the distance L153-V163 as a function of time, rather its
> > giving me some average distance of L153.
> >
>
> I don't understand what you mean. You can't have a distance of a point.
> Your
> syntax correctly specifies how to calculate a distance, so that's what you
> should be getting. Typically you'd use -oall for a simple distance, but
> that
> should probably be the same as -oav in the case of a single distance
> between two
> atoms.
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 26 May 2015 16:48:01 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] #include section in a .top file
> Message-ID: <5564DC01.8000704 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/26/15 8:57 AM, soumadwip ghosh wrote:
> > Plaese ignore the previous mail.
> >
> > Thanks Justin for your help as always. Actually, the atomtype CR was
> > common to both the building units of the polymer as well as the cation
> > built by SWISSPARAM. I generally dont use maxwarn at all but I too
> > thought of the warning being not harmful since the grompp was
> > complaining due to the atomtypes were same in two of the .itp files. I
> > would like to ask whether the construction of my .top file is right or
> > not. If in general, I have made two or more ligands from some other
> > source compatible with my force field , is the way I have mentioned
> > two atotypes.itp immediately after ff description is correct or not so
> > that I dont have to deal with this issue in future.
>
> Yes, it's fine.
>
> > Also, in the given context is it really possible to do something so
> > that gromacs does not show this 'overriding atomtypes' error? For once
> > I thought it would land me in different problems ( -maxwarn 1 option)
> > while running solvent relaxation and equilibration.
> >
>
> Like I said, and you've recognized above, you're not overriding anything.
> It's
> just redundant. If you don't want to see the warning, get rid of the
> redundancy. If different molecules share parameters, they only need to be
> declared once.
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 26 May 2015 16:49:28 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] trjconv command not found
> Message-ID: <5564DC58.7080300 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/26/15 12:38 PM, Poncho Arvayo Zatarain wrote:
> > Hello, when i use the command echo "0"|trjconv -f dppc128_1.xtc -s
> dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 i have this: command not found:
> trjconv. What can i do?
> >
>
>
> http://www.gromacs.org/Documentation/Installation_Instructions_5.0#getting-access-to-gromacs-after-installation
>
> If you're using the version 5.1 beta, there is no separate trjconv
> binary/link.
> Everything is in the gmx binary (gmx trjconv ...)
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 26 May 2015 16:50:11 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Index file
> Message-ID: <5564DC83.6020101 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/26/15 2:32 PM, Giannis Gl wrote:
> > Dear all,
> >
> > I am very amateur in GROMACS, so please forgive my silly question.
> > I want to group the following atoms
> >
> > ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00
> > 0.00
> > ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00
> > 0.00
> > ATOM 2285d N1 LIG X 6 32.318 58.744 110.532 0.00
> > 0.00
> > ATOM 2285e C2 LIG X 6 33.272 57.852 110.816 0.00
> > 0.00
> > ATOM 2285f N2 LIG X 6 34.376 58.450 111.368 0.00
> > 0.00
> > ATOM 22860 C3 LIG X 6 34.138 59.800 111.370 0.00
> > 0.00
> > ATOM 22861 C4 LIG X 6 35.550 57.768 111.896 0.00
> > 0.00
> > ATOM 22862 H1 LIG X 6 35.550 57.880 112.984 0.00
> > 0.00
> > ATOM 22863 H2 LIG X 6 35.460 56.692 111.730 0.00
> > 0.00
> > ATOM 22864 C5 LIG X 6 34.992 60.962 111.784 0.00
> > 0.00
> > ATOM 22865 H3 LIG X 6 35.626 61.290 110.956 0.00
> > 0.00
> > ATOM 22866 H4 LIG X 6 34.380 61.822 112.070 0.00
> > 0.00
> > ATOM 22867 O1 LIG X 6 35.840 60.652 112.888 0.00
> > 0.00
> > ATOM 22868 H5 LIG X 6 36.496 60.016 112.550 0.00
> > 0.00
> > ATOM 22869 C6 LIG X 6 33.084 56.380 110.604 0.00
> > 0.00
> > ATOM 2286a H6 LIG X 6 33.950 55.966 110.086 0.00
> > 0.00
> > ATOM 2286b H7 LIG X 6 33.040 55.868 111.568 0.00
> > 0.00
> > ATOM 2286c C7 LIG X 6 31.828 56.028 109.792 0.00
> > 0.00
> > ATOM 2286d H8 LIG X 6 30.938 56.388 110.312 0.00
> > 0.00
> > ATOM 2286e H9 LIG X 6 31.860 56.538 108.828 0.00
> > 0.00
> > ATOM 2286f C8 LIG X 6 31.688 54.518 109.558 0.00 0.00
> >
> > ...
> >
> > but the command,
> >
> > a 2285b-2286f
> >
> > or the command,
> >
> > a 2285b 2285c 2285d ... 2286f
> >
> > doesn't recognize atoms' numbers followed by a character
> >
> > "Found 0 atoms with names 2285B 2285C"
> >
> > Is there any other way that I could select these atoms?
> > I know I could try a dynamic selection (g_select), but unfortunately, my
> > pdb file contains 10 ligands and all of them have the same resname. Thus,
> > there is no feature besides the atom
> > that I could use to destinguish them. Even the coordinates are useless;
> > there are ligands with
> > almost the same x-coordinate but different y.
> > Thanking you in advance!
> > I hope I made clear my problem and didn't confuse you.
> >
>
> An index file expects integers, not letters. Number the coordinate file
> appropriately and you can do whatever analysis you want.
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 26 May 2015 14:52:00 -0600
> From: Eric Smoll <ericsmoll at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Molecule specific explosion
> Message-ID:
> <
> CALdrxPhNV9tqN4MXG37rDE+i14xp184BFcsa-EhvAiuTpGzLkQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Mark,
>
> Good question. I have rerun the simulation using a single molecule in a box
> without periodic boundary conditions and I see an identical distortion
> during energy minimization. Most of the suggestions present in
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up describe
> instability during MD. I am seeing this extreme geometry distortion much
> earlier during equilibriation.
>
> Best,
> Eric
>
> On Tue, Apr 28, 2015 at 3:38 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > What happens when you use this topology on a single molecule? Other
> > standard techniques for diagnosing at
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> >
> > Mark
> >
> > On Tue, Apr 28, 2015 at 8:09 AM, Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> > > Hi Mark,
> > >
> > > Thanks for the reply. In my previous message, one molecular component
> of
> > my
> > > liquid solution greatly-deforms ("explodes") on energy minimization. I
> > > have examined the topology and everything seems in order. No warnings
> > were
> > > generated by grompp or mdrun. Here are my minimization settings:
> > >
> > > constraints=h-bonds
> > > integrator=steep
> > > emtol=1000.0
> > > emstep=0.01
> > > nsteps=10000
> > > nstlist=10
> > > nstxout=1
> > > ns_type=grid
> > > rlist=1.5
> > > coulombtype=PME
> > > rvdw=1.5
> > > rcoulomb=1.5
> > > pbc=xyz
> > > cutoff-scheme=verlet
> > > nstcalclr=1
> > >
> > > The liquid topology file is generated by pdb2gmx using aminoacids and I
> > > detect no errors.
> > >
> > > Best,
> > > Eric
> > >
> > > On Sun, Apr 26, 2015 at 2:08 AM, Mark Abraham <
> mark.j.abraham at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Look at the whole molecule topology. Don't ignore any warnings.
> > > >
> > > > Mark
> > > > On 26/04/2015 9:38 am, "Eric Smoll" <ericsmoll at gmail.com> wrote:
> > > >
> > > > > Hello Gromacs Users,
> > > > >
> > > > > I have constructed a multi-component solution and, during energy
> > > > > minimization, one molecule type is radically deforming under ~ 0.2
> > ps.
> > > > All
> > > > > molecules of this type "explode" simultaneously. Looking over the
> > > > topology,
> > > > > all the atoms in this molecules appear to have correct forcefield
> > > > > assignments. I am writing to ask if anyone might have a suggestion
> on
> > > > how I
> > > > > can identify the origin of this problem.
> > > > >
> > > > > Best,
> > > > > Eric
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
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> > > > > posting!
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