[gmx-users] gromacs.org_gmx-users Digest, Vol 177, Issue 12
Tuanan Lourenço
lourenco.tuanan at gmail.com
Mon Jan 7 16:25:50 CET 2019
On Mon, Jan 7, 2019 at 7:07 AM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Selections in gromacs (Mark Abraham)
> 2. Re: Selections in gromacs (Mark Abraham)
> 3. inflategro2 (Netaly Khazanov)
> 4. Re: calculate angle between two beeta sheet (SHAHEE ISLAM)
> 5. Re: calculate angle between two beeta sheet (atanu das)
> 6. User defined tabulated potential for a particle with only
> repulsive interactions, in water (Braden Kelly)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 7 Jan 2019 00:28:07 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Selections in gromacs
> Message-ID:
> <CAMNuMARLyykzoU1JNX+c63YbnDO49B-gb=
> PY3yfMPrfnutEN5Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
>
Thank you very much for the answer Mark Abraham,
Maybe I did not explain myself well, one of the molecule is a simple
molecule that can move in the whole box, but the another molecule is
frozen, so this molecule has a specific position in the box.
I would like to get the diffusion coefficient of the "free" molecule just
when it is interacting with the frozen molecule (close to). Something to
the diffusion coefficient close to a surface or layer.
Thank you very much
Hi,
>
> If it's the same two molecules each time, then you can use a static index
> group. Is it?
>
> Mark
>
> On Sun, Jan 6, 2019 at 8:41 PM Tuanan Louren?o <lourenco.tuanan at gmail.com>
> wrote:
>
> > Hi everyone,
> >
> > I am trying to use the "gmx trjconv" to write a new trajectory from my
> > "main trajecetory" that contains just two molecules then they are close
> to
> > each other in a specific distance. The idea is to have a new trajectory
> > that contains these molecules in this specific distance in each frame and
> > use this to calculate different properties such as msd. I also tried to
> use
> > the "gmx select" with the option -ofpdb but this writes just an average
> of
> > the positions, not for each frame. Has someone has some idea about how I
> > can proceed?
> >
> > Thank you
> > --
> > __________________________________________________
> > MSc. Tuanan C Louren?o
> > Ph.D Student Physical Chemistry - Universidade Federal Fluminense
> > Molecular Modelling and Computer Simullation Group - UFF
> > MOLMOD-CS WEBSITE <http://www.molmodcs.uff.br/>
> > --
> > 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
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> > send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 7 Jan 2019 00:28:07 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Selections in gromacs
> Message-ID:
> <CAMNuMARLyykzoU1JNX+c63YbnDO49B-gb=
> PY3yfMPrfnutEN5Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> If it's the same two molecules each time, then you can use a static index
> group. Is it?
>
> Mark
>
> On Sun, Jan 6, 2019 at 8:41 PM Tuanan Louren?o <lourenco.tuanan at gmail.com>
> wrote:
>
> > Hi everyone,
> >
> > I am trying to use the "gmx trjconv" to write a new trajectory from my
> > "main trajecetory" that contains just two molecules then they are close
> to
> > each other in a specific distance. The idea is to have a new trajectory
> > that contains these molecules in this specific distance in each frame and
> > use this to calculate different properties such as msd. I also tried to
> use
> > the "gmx select" with the option -ofpdb but this writes just an average
> of
> > the positions, not for each frame. Has someone has some idea about how I
> > can proceed?
> >
> > Thank you
> > --
> > __________________________________________________
> > MSc. Tuanan C Louren?o
> > Ph.D Student Physical Chemistry - Universidade Federal Fluminense
> > Molecular Modelling and Computer Simullation Group - UFF
> > MOLMOD-CS WEBSITE <http://www.molmodcs.uff.br/>
> > --
> > 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: 3
> Date: Mon, 7 Jan 2019 08:44:10 +0200
> From: Netaly Khazanov <netalyk at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] inflategro2
> Message-ID:
> <CAGR0SZF_7i0ZaxyevjuePYRd_=
> t_tH4U-7cgLJXU3XqVDeOjDw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi All,
> My membrane contains a mixture of DPPC and DOPC lipids and aligned protein.
> I am trying to insert protein into the membrane using inflategro2 scripts.
> During the running the script is writing:
> Deep recursion on subroutine "main::dynInflating" at
>
> /home/gnss/netaly/FL_CFTR_Cduction/onelayer/Healthy_membrane_DPPC_DOPC_new/inflategro2_rc1/inflategro2_rc1/tegro2_org
> line 736, <STDIN> line 3.
> Used an inflating factor of 17.7 to solve protein-lipid overlaps
> And the output inflated.gro file showed that dynamic lipids weren't scaled
> back and retained detached from the membrane.
> inflategro2_org -f protein_ATP_membrane_box1.gro -n index.ndx -p topol.top
> -m deflate_org.mdp -v
> Any help will be appreciated!
> Thanks,
> Netaly Khazanov
>
>
> --
> Netaly
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 7 Jan 2019 12:44:58 +0530
> From: SHAHEE ISLAM <islamshahee at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] calculate angle between two beeta sheet
> Message-ID:
> <
> CAJZ7aT9dXHY1oAPoRMHcmhZqQH-a-CkTAcnCWYOjUKq0yhAFLw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> can anyone please help me in this regards.
>
> On 1/4/19, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> > hi,
> > my protein contain three beeta sheet.
> > (i) resid 43-45
> > (ii) resid 51-53
> > (iii) resid 58-59
> > i want to calculate the angle between two beeta sheet.can any one
> > please suggest me how i can do this.
> > thanking you
> > shahee
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 7 Jan 2019 07:21:31 +0000 (UTC)
> From: atanu das <samrucu at yahoo.co.in>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] calculate angle between two beeta sheet
> Message-ID: <1678551364.13292976.1546845691336 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> First define the two vectors e.g. select the c-alphas of residues 43 and
> 45 (vector1) and residues 51 and 53 (vector2). Then calculate the angle
> between the two vectors (possibly using the command g_sgangle). This will
> give you a time series of the angle between the two above-mentioned
> vectors.Atanu
>
> Sent from Yahoo Mail on Android
>
> On Mon, Jan 7, 2019 at 12:45 PM, SHAHEE ISLAM<islamshahee at gmail.com>
> wrote: can anyone please help me in this regards.
>
> On 1/4/19, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> > hi,
> > my protein contain three beeta sheet.
> > (i) resid 43-45
> > (ii) resid 51-53
> > (iii) resid 58-59
> > i want to calculate the angle between two beeta sheet.can any one
> > please suggest me how i can do this.
> > thanking you
> > shahee
> >
> --
> 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
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>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 7 Jan 2019 09:05:30 +0000
> From: Braden Kelly <bkelly08 at uoguelph.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] User defined tabulated potential for a particle
> with only repulsive interactions, in water
> Message-ID:
> <
> YQXPR0101MB14320C03003E84D80AA67C2AD2890 at YQXPR0101MB1432.CANPRD01.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I would like to simulate a particle that has only a repulsive (no
> attraction) terms in its potential energy interaction with all other
> particles. I am simulating this particle in tip3p water.
>
>
> I am trying to use the tabulated potential option since I know its
> potential form, and force as well. In python lingo the potential and force
> are
>
>
> def cavityPot(r):
> pot = potA * np.exp(-r/potB + Lambda )
> return pot
> def cavityForce(r):
> force = - potA / (-potB) * np.exp( -r/potB + Lambda )
> return force
>
> potA = 1255 # kj/mol
>
> potB = 0.1 # nm
>
> Lambda = -2
>
> r = distance between two atoms, nm
>
>
> The simulation does run, but is not correct and terminates prematurely,
> but without raising an error. I say this because the energy minimization
> converges in around 10 steps which does not happen even for a simulation
> with only water in it, and the NVT equilibration starts without error,
> runs, but quits without actually running i.e., the atom coordinates are the
> same after as before.
>
>
> Unfortunately there is no error during running, so I must show my files
> and explain my procedure, and hope a flaw is picked out of these. One note
> is that gromacs complains that the force it calculates is 52% different
> from my tabulated force. The equation is analytical, the derivative of
> potential energy is straightforward. When I test it numerically as well, I
> still get results saying my force/energy are correct. Some values from a
> table are shown near the bottom.
>
>
> If you are still reading, I will go into more depth on my topology,mdp
> file used, and table generation: here is the top portion of the .top file
>
>
> ---------------------------------------------------------------
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5 0.8333
>
> [ atomtypes ]
> ; name mass charge ptype sigma(nm) epsilon(kJ/mol)
> ; tip3p atoms
> OW OW 15.99940 -0.8340 A 0.315061 0.6364000
> HW HW 1.008000 0.4170 A 0.0000 0.0000000
>
>
> ;name bond_type mass charge ptype sigma epsilon
> CAV CAV 0.00000 0.00000 D 0.000000 0.000000 ;
>
> [ nonbond_params ] ; for tabulated potential A and C parameters need to be
> set to 1
> ; i j func V(c6) W(c12)
> CAV OW 1 1 1
> CAV HW 1 1 1
>
> ;=====================================================================
> ; CAVITY - DUMMY
> ;=====================================================================
> ; Include CAVITY topology
> #include "CAVITY_GMX.itp"
>
> ;=====================================================================
> ; WATER tip3p
> ;=====================================================================
> [ moleculetype ]
> ; molname nrexcl
> SOL 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> 1 OW 1 SOL OW 1 -0.8340 15.99940
> 2 HW 1 SOL HW1 2 0.4170 1.0080
> 3 HW 1 SOL HW2 3 0.4170 1.0080
>
> (Removed rest of tip3p info to save space... it involves settles etc)
> ;=====================================================================
> [ system ]
> CAVITY in Water
>
> [ molecules ]
> CAVITY 1
> SOL 500
>
> --------------------------------------------------------------------------------------------------------
> The corresponding #include "CAVITY_GMX.itp" is
>
> --------------------------------------------------------------------------------------------------------
> [ moleculetype ]
> ; Name nrexcl
> CAVITY 3
>
> [ atoms ] ;
> ; nr type resi res atom cgnr charge mass ; qtot
> bond_type
> 1 CAV 1 CAV CAV 1 0.0000 0.00000 ;
>
> --------------------------------------------------------------------------------------------------------
> The mdp parameters I use in addition to a typical minimization/NVT run is:
>
>
> --------------------------------------------------------------------------------------------------------
>
> cutoff-scheme = group
>
> ; USER DEFINED POTENTIAL TABLES
> energygrps = CAV OW HW1 HW2
> energygrp_table = CAV OW CAV HW1 CAV HW2
> table-extension = 1 ; Extension of the potential
> lookup tables beyond the cut-off
> ; Electrostatics
> coulombtype = PME-User
> ; method for vdW (LJ)
> vdwtype = user
>
> --------------------------------------------------------------------------------------------------------
>
> For the NVT run i use deffnm = NVTEq, so my tables are respectively called
>
> NVTEq.xvg, NVTEq_CAV_CAV.xvg,
> NVTEq_CAV_OW.xvg,NVTEq_CAV_HW1.xvg,NVTEq_CAV_HW2.xvg
>
>
> All tables are the same since the cavity does not care what particle it is
> interacting with and looks like
>
>
>
> ---------------------------------------------------------------------------------------------------------
>
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0345582 0.3455824
> 0.0020000 0.0000000 0.0000000 0.0000000 0.0000000 0.0338739 0.3387394
> 0.0040000 0.0000000 0.0000000 0.0000000 0.0000000 0.0332032 0.3320320
> 0.0060000 0.0000000 0.0000000 0.0000000 0.0000000 0.0325457 0.3254573
> 0.0080000 0.0000000 0.0000000 0.0000000 0.0000000 0.0319013 0.3190128
> 0.0100000 0.0000000 0.0000000 0.0000000 0.0000000 0.0312696 0.3126959
> 0.0120000 0.0000000 0.0000000 0.0000000 0.0000000 0.0306504 0.3065041
> (and so on to the r = 2.5)
>
>
> I make an index file with groups [ system ], OW, HW1,HW2, CAV.
>
>
> I call gromacs using
>
> gmx grompp -c aqueous.g96 -p run.top -f index.ndx -maxwarn 2 -o NVTEq.tpr
> gmx mdrun -deffnm NVTEq -table NVTEq.xvg -c aqueous.g96
>
>
> To recap, the energy minimization runs but stops way to soon. The NVT
> runs, but doesn't actually seem to do anything. The coordinates are not
> updated and it stops right away. No errors are generated.
>
>
> I appreciate any help,
>
>
> Braden
>
>
> ------------------------------
>
> --
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>
> End of gromacs.org_gmx-users Digest, Vol 177, Issue 12
> ******************************************************
>
--
__________________________________________________
MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE <http://www.molmodcs.uff.br/>
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