[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 61
Sanket Ghawali
sanket.ghawali at gmail.com
Wed May 18 06:40:55 CEST 2016
Message: 3
Date: Mon, 16 May 2016 07:51:51 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Calculating Distance
Message-ID: <ae63ebfd-090e-65a3-901b-5fd99655edd8 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 5/16/16 3:20 AM, Sanket Ghawali wrote:
> Dear, gmx-users,
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I visualize the trajectory in VMD, the peptide moves to the SDS
> interface where initially it was placed in the center, the results
> are as expected. I would like to calculate the distance the peptide
> has traveled or moved from the center to the interface
>
>
> Any suggestions on how to go about doing this?
>
Calculating distances is what the gmx distance program is for. Simply
obtain
the COM distance between the micelle and peptide (or any subset of atoms
that
makes sense).
-Justin
Thank you Justin. I am sorry, I didn't make my query specific.
g_dist calculates distance between COMS of 2 groups with reference to time.
I want to monitor the change in the COM of the peptide with respect to the
initial position (COM) of the peptide at 0ns and not between COM of 2
different groups with reference to time.
Please help me with "how to fix the reference position for distance
calculation"
Greatly appreciate your help and do let me know if I need to explain the
query further
With regards,
Sanket.
On Mon, May 16, 2016 at 8:56 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. heat of vaporization (Saitama Lawliet)
> 2. Re: simulation_time (Justin Lemkul)
> 3. Re: Calculating Distance (Justin Lemkul)
> 4. tutor/speptide (Alexander Alexander)
> 5. Re: tutor/speptide (Justin Lemkul)
> 6. improper .gro file format generated by trjconv (Esra Ka?ar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 May 2016 16:35:02 +0530
> From: Saitama Lawliet <feynman375 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] heat of vaporization
> Message-ID:
> <CANKpOi=UXmqUy20ya+nWa30GGVTWVkOjKEQTrDLZ3oQLj7A4=
> g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all
>
> I am trying to calculate heat of vaporization of tri-ethyl phosphate (tep).
> I took 500 tep molecules for MD simulation. After energy minimization and
> NVT I performed NPT simulation for 10ns with usual PBC, dispersion
> correction etc.
> >From the final results using g_energy -nmol 500 I got the potential energy
> of -155.406kj/mol.
> The density of the liquid tep was 1085.8kg/m3 which is very close to the
> earlier MD reported data.
> Then I took one single tep molecule in a box and perform the calculation
> without using pbc and all cut-off to zero. The potential energy I got was
> -692.13kj/mol.
>
> Now as per defintion of HVap= U(gas)- U(liquid) +RT
> I am getting the value of Hvap of tep as: -534.25kj/mol whereas the
> reported value is 77.69kj/mol. what is wrong I am unable to find out.
> Any help to sort out this mistake will be highly appreciated.
>
> warm regards
>
> APJ
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 16 May 2016 07:50:38 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] simulation_time
> Message-ID: <ff391d97-2261-54db-5073-d3b141d223c6 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/16/16 12:23 AM, Ms. Nikita Bora wrote:
> > ---------------------------- Original Message
> ----------------------------
> > Subject: Re: simulation_time
> > From: "Ms. Nikita Bora" <niki24 at tezu.ernet.in>
> > Date: Mon, May 16, 2016 9:42 am
> > To: niki24 at tezu.ernet.in
> >
> --------------------------------------------------------------------------
> >
> > Respected Sir,
> >
> > Thanks for the reply. I would further like to know that according to this
> > tutorial
> > (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> )
> > the rvdw=rcoulomb=1 is used for the protein while according to this
> > tutorial
> > (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> )
> > rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
> > and protein-ligand complex is used??
> >
>
> Different force fields, different settings.
>
> -Justin
>
> >
> >> Respected Sir,
> >>
> >> Recently i followed your tutorial for simulation of a 50 ns final mdrun
> > of protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used.
> > The simulation runned at aorund 10 ns/day . While for the same complex
> > when rvdw=rcoulomb=1 is made the run was 10 ns/day.
> >>
> >> Sir i would like to know is there any standard value for rvdw,rcoulomb
> > and why a longer time is taken for 1.4 value
> >>
> >>
> >> ___________________
> >> D I S C L A I M E R
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> >>
> >
> >
> >
> > ___________________
> > D I S C L A I M E R
> > This e-mail may contain privileged information and is intended solely for
> > the individual named. If you are not the named addressee you should not
> > disseminate, distribute or copy this e-mail. Please notify the sender
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> > secure or error-free as information could be intercepted, corrupted,
> > lost, destroyed, delayed, or may contain viruses. The recipient must
> > verify the integrity of this e-mail message.
> >
> >
> >
> >
> > ___________________
> > D I S C L A I M E R
> > This e-mail may contain privileged information and is intended solely for
> > the individual named. If you are not the named addressee you should not
> > disseminate, distribute or copy this e-mail. Please notify the sender
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> > deliver error free e-mail messages but it can not be guaranteed to be
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> > or error-free as information could be intercepted, corrupted, lost,
> destroyed,
> > delayed, or may contain viruses. The recipient must verify the integrity
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> > this e-mail message.
> >
>
> --
> ==================================================
>
> 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: Mon, 16 May 2016 07:51:51 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Calculating Distance
> Message-ID: <ae63ebfd-090e-65a3-901b-5fd99655edd8 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/16/16 3:20 AM, Sanket Ghawali wrote:
> > Dear, gmx-users,
> >
> > Hello everyone,
> > I'm simulating a peptide in an SDS micelle. The simulation was
> > performed for 100ns
> > When I visualize the trajectory in VMD, the peptide moves to the SDS
> > interface where initially it was placed in the center, the results
> > are as expected. I would like to calculate the distance the peptide
> > has traveled or moved from the center to the interface
> >
> >
> > Any suggestions on how to go about doing this?
> >
>
> Calculating distances is what the gmx distance program is for. Simply
> obtain
> the COM distance between the micelle and peptide (or any subset of atoms
> that
> makes sense).
>
> -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: Mon, 16 May 2016 15:51:08 +0200
> From: Alexander Alexander <alexanderwien2k at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] tutor/speptide
> Message-ID:
> <
> CAEDv6u6JvUjDCcgv97B0nA9ZjMDtFuRa-Ge05RWyc9Yv6JkKBg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs user,
>
> In below link where the S-peptide has been taught for the beginner, they
> point out that the tutorial materials have been stored in the directory
> "tutor/speptide", would you please let me know where I can find this
> directory or have access to this directory?
>
> http://manual.gromacs.org/archive/4.6.6/online/speptide.html
>
> Thanks,
> Cheers,
> Alex
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 16 May 2016 09:54:55 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] tutor/speptide
> Message-ID: <b8a0f3b0-afb6-77fd-ab8e-8978594479e5 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/16/16 9:51 AM, Alexander Alexander wrote:
> > Dear Gromacs user,
> >
> > In below link where the S-peptide has been taught for the beginner, they
> > point out that the tutorial materials have been stored in the directory
> > "tutor/speptide", would you please let me know where I can find this
> > directory or have access to this directory?
> >
> > http://manual.gromacs.org/archive/4.6.6/online/speptide.html
> >
>
> Outdated documentation. The "tutor" subdirectory was removed prior to
> version
> 4.6 as it was generally not very useful and therefore undesirable to
> maintain.
> Comprehensive tutorials are linked on the GROMACS webpage.
>
> -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: 6
> Date: Mon, 16 May 2016 18:26:27 +0300
> From: Esra Ka?ar <esrakacar at iyte.edu.tr>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] improper .gro file format generated by trjconv
> Message-ID:
> <CAArOx8JEB_QCTkOm5=
> JUqEncE037JY7WJTuHKW6kuFB7ZT3a9Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gromacs users;
>
> I am trying to perform micelle clustering analysis as described in gromcas
> website:
>
> 1. use trjconv
> <http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv> -pbc
> cluster to obtain a single frame that has all of the lipids in the unit
> cell. This must be the first frame of your trajectory. A similar frame
> from
> some previous timepoint will not work.
> 2. use grompp
> <http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp> to make
> a new tpr file based on the frame that was output from the step above.
> 3. use trjconv
> <http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv> -pbc
> nojump to produce the desired trajectory using the newly produced tpr
> file.
>
> Firstly I am trying to use trjconv to have a .gro file, but the output of
> first step gives me a .gro file in improper format, i.e.coordinates are not
> written with required spaces between each other. Here is my command line:
>
> gmx trjconv -f mytrajectory.xtc -o micelle.gro -s mytopology.tpr -e 0.001
> -pbc cluster
>
> And here is the micelle.gro file:
>
> 1CHOA ROH 1 2.7 8.2 7.7
> 1CHOA R1 2 3.0 8.1 7.7
> 1CHOA R2 3 3.2 8.1 7.8
> 1CHOA RO2 4 3.2 7.8 7.7
> 1CHOA RO3 5 3.4 7.8 7.9
> 1CHOA R3 6 3.4 7.8 7.7
> 1CHOA C1 7 3.6 7.5 7.7
> 1CHOA OCO 8 3.5 7.1 7.6
>
> What can be the possible reason for this error and how can I fix it?
>
> With regards,
> Esra
>
>
> ------------------------------
>
> --
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