[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 55

Antara mazumdar antara.mazumdar at igib.in
Sun May 15 10:48:56 CEST 2016


Dear Justin,

I am using the velocities from the NPT run. Could you please explain on the
.cpt file you mentioned?

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Sun, May 15, 2016 at 10:51 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. COM-Pull along a direction (Pengzhi Zhang)
>    2. Re: error in running mdrun of membrane protein in a mixed
>       bilayer with MARTINI MODEL (Justin Lemkul)
>    3. Umbrella Sampling - choice of pull-coord?-dim (Lukas Zimmermann)
>    4. PCA and FEL (sun)
>    5. Re: PCA and FEL (Tsjerk Wassenaar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 14 May 2016 14:58:37 -0500
> From: Pengzhi Zhang <pzhang5 at central.uh.edu>
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] COM-Pull along a direction
> Message-ID: <5737836D.8010409 at central.uh.edu>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> Dear Gromacs users,
>
> I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull
> the ion along specific pre-determined paths.
>
>  From my understanding, pulling along a direction _V guarantees that the
> dumb bead would move only at direction _V. The position of the dumb bead
> is simply: _r(t) = _r(0) + _V*speed*time (_ means vector). And if the
> spring constant is sufficiently large, the pulled atom (a single ion)
> would also follow the dumb bead (with fluctuations). However, I found
> that no matter how large the spring constant is (I vary it from 100 to
> 1,000,000 kJ/mol/nm**2), the pulled atom deviates from the direction _V
> in a certain amount of time (usually after the pulled bead unbinds),
> sometimes it even goes perpendicular to _V and moves out of the box,
> terminating the simulation.
>
> Does the direction _V (pull-coord1-vec) mean the direction of
> instantaneous pull force or the direction of the path that the dumb bead
> follows?
>
> Thank you very much in advance!
>
>
> Here is the pull part of my mdp file.
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant-force
> pull                            = umbrella
> pull-geometry            = direction
> pull-ngroups              = 2
> pull-ncoords              = 1
> pull-group1-name      = binding_site_atoms
> pull-group2-name      = pull_ion           ; pull group
> pull-start                    = yes
> pull-coord1-vec          = -0.07 -0.04 0.99
> pull-coord1-groups    = 1 2
> pull_coord1_rate        = 0.001        ; nm/ps
> pull-coord1-k             = 10000       ; kJ/mol/nm^2
> pull-nstxout               = 10         ; 0.02 ps
> pull-nstfout                = 10
> pull-print-reference    = yes
>
>
> Sincerely,
> Pengzhi
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 14 May 2016 18:33:08 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] error in running mdrun of membrane protein in
>         a mixed bilayer with MARTINI MODEL
> Message-ID: <5b732333-0517-e66f-2e4b-7a9cf337e3d9 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/14/16 2:34 PM, Mark Abraham wrote:
> > Hi,
> >
> > Please keep the discussion on the mailing list, so others can help and
> > learn.
> >
> >> Antara said:
> >> I have pasted the mdrun command i used to run it in parallel with the
> > number of processors i used which was 16. The command is :
> >>
> >>
> >> /app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8
> >
> > That still isn't a command you've copied and pasted from a terminal or a
> > script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
> > etc.
> >
> >> In the pbs script, i used 16 in the number of processors option.
> >
> > What happens when you run on one rank?
> >
> >> For the production tpr, i used the gro file from the last equilibration
> > step(step6.6) The command used was :
> >>
> >> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
> > MD.mdp -o MD.tpr
> >
> > That looks like it could be reasonable, but as with any equilibration you
> > need to look at observables to judge that it's equilibrated. Their
> builder
> > should provide reasonable defaults, but you can't assume they're perfect,
> > either. In particular, if the last equilibration ensemble doesn't match
> the
> > production ensemble, that could be the problem.
> >
>
> Failing to pass the .cpt file to grompp -t after equilibration is a great
> way to
> do that.  The production simulation is starting from some unpredictable
> ensemble, without velocities, etc..
>
> -Justin
>
> > Mark
> >
> > On Sat, May 14, 2016 at 5:10 PM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar <
> antara.mazumdar at igib.in>
> >> wrote:
> >>
> >>> Dear users,
> >>>
> >>> I am trying to run a coarse grained simulation of a membrane protein
> in a
> >>> mixed lipid billayer using martini model 2.2. I have already performed
> all
> >>> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> >>> However, when i try to execute its production run in parallel(having
> >>> gromacs 5.1 version installed)  it complains of LINCS warning and
> >>> terminates at step 0. The lincs warning error is coming from BB and SC1
> >>> atoms of one of the protein residues.
> >>>
> >>
> >> There are lots of possible places to go wrong, including not making your
> >> production .tpr based on the outputs of your equilibration. This seems
> >> quite a likely possibility.
> >>
> >> You should also consider further equilibration - whether using Martini
> or
> >> not, it is sometimes necessary to use a small time step when relaxing
> >> problem configurations.
> >>
> >>
> >>>  But on the contrary, it runs on the desktop successfully. *My
> production
> >>> run mdp file details are below :*
> >>>
> >>>
> >>> .
> >>>
> >>> This is the MD.mdp file :ntegrator               = md
> >>> tinit                    = 0.0
> >>> dt                       = 0.020
> >>> nsteps                   = 2500000000
> >>>
> >>> nstxout                  = 2000
> >>> nstvout                  = 2000
> >>> nstfout                  = 2000
> >>> nstlog                   = 2000
> >>> nstenergy                = 2000
> >>> nstxtcout                = 2000
> >>> xtc_precision            = 100
> >>>
> >>> ns_type                  = grid
> >>> pbc                      = xyz
> >>> nstlist                 = 10
> >>> cutoff-scheme           = Verlet
> >>> rlist                   = 1.2
> >>> vdwtype                 = Cut-off
> >>> vdw-modifier            = none
> >>> rvdw_switch             = 1.0
> >>> rvdw                    = 1.2
> >>> coulombtype             = pme
> >>> rcoulomb                = 1.2
> >>>
> >>> tcoupl                   = v-rescale
> >>> tc-grps                  = protein CHOL_POPC_DPSM_DPCE W_ION
> >>>
> >>> tau_t                    = 1.0 1.0  1.0
> >>> ref_t                    = 303.15 303.15 303.15
> >>>
> >>> ; Pressure coupling:
> >>> Pcoupl                   = berendsen
> >>> Pcoupltype               = semiisotropic
> >>> tau_p                    = 5.0  5.0
> >>> compressibility          = 3e-4 3e-4
> >>> ref_p                    = 1.0  1.0
> >>> ; GENERATE VELOCITIES FOR STARTUP RUN:
> >>> gen_vel                  = no
> >>> refcoord_scaling         = all
> >>>
> >>> *the command used for mdrun :*
> >>>
> >>> -deffnm MD -pin on -rdd 1.8 -np 16
> >>>
> >>
> >> mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
> >> Please don't edit and filture things, copy and paste whole actual
> things.
> >> :-)
> >>
> >> Mark
> >>
> >> I would also like to mention that i generated the initial structure of
> the
> >>> system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
> >>> have followed the exact builder protocol for the equilibration and
> >>> minimisation.
> >>>
> >>> Kindly suggest something!
> >>>
> >>> Thanks,
> >>> Antara
> >>>
> >>> --
> >>> Junior research fellow(project)
> >>> Systems biology group
> >>> CSIR-Institute of Genomics & Integrative Biology
> >>> South Campus
> >>> New Delhi -  110020
> >>> M : +91-9717970040
> >>> --
> >>> --
> >>> 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 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: Sun, 15 May 2016 00:55:23 +0200
> From: Lukas Zimmermann <luk.zim91 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Umbrella Sampling - choice of pull-coord?-dim
> Message-ID:
>         <CAPSKXTqEZw4=
> 1CcAB3fTBPVTZFvRZLghz6D5eCQ1Yaq2yTgX4w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear GROMACS users,
>
> I am interested in the role of the mdp parameter pull-coord?-dim when
> sampling
> a particular umbrella window after having generated initial configurations
> for, say, the
> COM distance between two groups being the reaction coordinate.
>
> I know that these options can be controlled to restrict the actual pulling,
> say with geometry distance,  to a subset of the pull vector components, for
> instance to enable
> aligment of the pull vector with the box dimensions.
>
> However, I do not understand its role when performing umbrella sampling
> along the reaction coordinate.
> I know that the pull-code then controls the COM distance between the pull
> groups with a (usually) harmonic potential, but what effect will
> pull-coord?-dim have?
>
> I observe different behavior for my toy system consisting of two methanol
> molecules in vacuum.
> With all components enables, I need to correct the PMF for entropic
> decrease in the PMF,
> since the methanol is sampled on a sphere with increasing radius.
> If only allowing one component, the PMF will be flat, but different values
> for delta G
> result.
>
> Also, in the US Tutorial by Justin, the US code uses:
>
> pull_coord1_dim         = N N Y
>
> Is there any particular reason, not to set
>
> pull_coord1_dim         = Y Y Y
>
> here? Would this setting also be justified? Since, as far as I understood
> the procedure,  pulling
>
> is just there for generating the initial configurations and US is more or
> less independent of this.
>
>
>
> Many thanks in advance!
>
> Lukas
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 15 May 2016 09:03:34 +0530
> From: sun <sun.iba2 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] PCA and FEL
> Message-ID: <EC81EF15-0FCC-4BA7-B3AA-84D789822105 at gmail.com>
> Content-Type: text/plain;       charset=us-ascii
>
> Hello everyone
> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
> for the stability of my pro-lig complex.   In a 2015 paper, The group
> calculated two principal component, PC1 and PC2 and then prepared an.xvg
> file to be used as input for g_sham. My question is, when we use g_anaeig;
> we get eigenvec.xvg. from -comp flag. Now how shall one select two
> principal components from that data? I am sorry if my question is wrong but
> please help me.
>
> My second question is, can we use any two parameters like rmsd and Rg for
> input in g_sham to probe the stability of complex? Is that valid?
>
> With Regards
> Suniba
>
> Sent from my iPhone
>
> ------------------------------
>
> Message: 5
> Date: Sun, 15 May 2016 07:21:37 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] PCA and FEL
> Message-ID:
>         <
> CABzE1Sg4eZ1YtdBJsMC_Z-x3hOn3U1zqv74CoF4nSoaykss1BQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Suniba,
>
> No, with gmx anaeig you can select -2d, which does a 2D projection onto the
> selected eigenvectors. Alternatively, you can combine any two projections
> onto eigenvectors, which you get using the option -proj. The quickest way
> to do that is something like:
>
> paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
> combined.xvg
>
> You will loose the labels, but that should be fine.
>
> You can combine other variables in a similar manner.
>
> Hope it helps,
>
> Tsjerk
>
> On Sun, May 15, 2016 at 5:33 AM, sun <sun.iba2 at gmail.com> wrote:
>
> > Hello everyone
> > I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
> > for the stability of my pro-lig complex.   In a 2015 paper, The group
> > calculated two principal component, PC1 and PC2 and then prepared an.xvg
> > file to be used as input for g_sham. My question is, when we use
> g_anaeig;
> > we get eigenvec.xvg. from -comp flag. Now how shall one select two
> > principal components from that data? I am sorry if my question is wrong
> but
> > please help me.
> >
> > My second question is, can we use any two parameters like rmsd and Rg for
> > input in g_sham to probe the stability of complex? Is that valid?
> >
> > With Regards
> > Suniba
> >
> > Sent from my iPhone
> > --
> > 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.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> End of gromacs.org_gmx-users Digest, Vol 145, Issue 55
> ******************************************************
>


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