[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 1
Seera Suryanarayana
palusoori at gmail.com
Tue Dec 2 07:17:03 CET 2014
Dear Mark
I have used the following command.
gmx rms -s em.tpr -f em.trr -o rmsd.xvg
I got nothing the graph. You can find the graph in the attachment
Surya
Graduate student
India.
On Mon, Dec 1, 2014 at 4:24 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Electrostatic force cutoffs (Mark Abraham)
> 2. Position Restraint or remove COM from DNA (Hovakim Grabski)
> 3. Re: Position Restraint or remove COM from DNA (Justin Lemkul)
> 4. Can we calculate rmsd from after energy minimization?
> (Seera Suryanarayana)
> 5. Re: Can we calculate rmsd from after energy minimization?
> (Mark Abraham)
> 6. error in PME mesh load (RINU KHATTRI)
> 7. Re: error in PME mesh load (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 30 Nov 2014 20:45:12 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Electrostatic force cutoffs
> Message-ID:
> <
> CAMNuMATwkfZM+wx-w_K6OLheOwuhE894Com5KLZPmBhnZ3reYQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
>
> On Sun, Nov 30, 2014 at 6:47 PM, Nathan K Houtz <nhoutz at purdue.edu> wrote:
>
> > Hello all,
> >
> > I'm wondering if gromacs will allow me to use either a wolf electrostatic
> > cutoff method or a damp shifted force cutoff method, similar to what is
> > described by C. J. Fennell (2006). (I think the paper is:
> >
> http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581)
>
>
> I'm not familiar with any of the above, but if it involves only two-body
> interactions, then it is straightforward to implement with tabulated
> interactions without touching the code (currently only available with the
> group cut-off scheme). If it involves anything else, and is not an easily
> expressed modification of something you can find in the manual, then it is
> probably prohibitively difficult. I guess that's your homework :-)
>
>
> > If so, are there any tutorials or how-to's on how to implement them?
> >
>
> No. Implementing a high-performance MD implementation is invariably a
> custom job, but if you can answer the above questions, then we can point
> you in the right directions.
>
> Mark
>
>
> > If it matters, I am attempting to simulate tetrolic acid (also called
> > 2-butynoic acid) in a solution of water (Tip3p).
> >
> > Thanks very much for your help!
> > N.H.
> > --
> > 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: 2
> Date: Sun, 30 Nov 2014 20:27:29 +0000 (UTC)
> From: Hovakim Grabski <hovakim_grabski at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] Position Restraint or remove COM from DNA
> Message-ID:
> <
> 346439401.1728836.1417379249165.JavaMail.yahoo at jws10027.mail.ne1.yahoo.com
> >
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs Users,I'm trying to run a simulation between a Dickerson
> dodecamer(12 basepair DNA) and 6 molecules of Methylene Blue.My ?1 question
> is:
> If I try to ?remove COM from DNA, it gives an error, so I have to
> set?comm_grps ?= System, but?1) doesn't that affect the Methylene Blue
> molecules?2) is there any way to ?remove COM from DNA without getting an
> error?
> 2. Or should I just use position restraint on DNA's 5' and 3' ends on one
> strand?
> Thanks in advance,Hovakim
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 30 Nov 2014 16:08:18 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org, Hovakim Grabski <hovakim_grabski at yahoo.com>
> Subject: Re: [gmx-users] Position Restraint or remove COM from DNA
> Message-ID: <547B8742.5080609 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/30/14 3:27 PM, Hovakim Grabski wrote:
> > Dear Gromacs Users,I'm trying to run a simulation between a Dickerson
> dodecamer(12 basepair DNA) and 6 molecules of Methylene Blue.My 1 question
> is:
> > If I try to remove COM from DNA, it gives an error, so I have to set
> comm_grps = System, but 1) doesn't that affect the Methylene Blue
> molecules?2) is there any way to remove COM from DNA without getting an
> error?
> > 2. Or should I just use position restraint on DNA's 5' and 3' ends on
> one strand?
>
> What purpose is there in introducing such artificiality?
>
> There is no sensible reason to only remove COM motion from part of the
> system
> during the simulation (and you actually run the risk of the simulation
> crashing
> due to artifacts for solute-in-water systems). Only in interfacial
> systems with
> components having different diffusion coefficients does it really make
> sense to
> specify separate groups.
>
> -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, 1 Dec 2014 11:49:03 +0530
> From: Seera Suryanarayana <palusoori at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Can we calculate rmsd from after energy
> minimization?
> Message-ID:
> <
> CAAr94NNxOz3nq8yxssAGofHGvX-4cqzcJ7N53CLVHsdR4hyMWw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs Users
>
> I would like to know whether it possible to calculate rmsd immediately
> after energy minimization step, in other words from em.tpr and em.trr file.
>
> I tried to calculate the rmsd by using above mentioned files, but I have
> got nothing.
>
> If it is possible to calculate the rmsd from the energy minimized
> structure, kindly tell me how do we do it.
>
> Thanks in advance
> Surya
> Graduate student
> India.
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 1 Dec 2014 08:40:11 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Can we calculate rmsd from after energy
> minimization?
> Message-ID:
> <CAMNuMARZPT_TK=pBV8YP3d4-Ko4WQ=Y=1b=zK9JRPq1RL=
> w44A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Dec 1, 2014 at 7:19 AM, Seera Suryanarayana <palusoori at gmail.com>
> wrote:
>
> > Dear Gromacs Users
> >
> > I would like to know whether it possible to calculate rmsd immediately
> > after energy minimization step, in other words from em.tpr and em.trr
> file.
> >
> > I tried to calculate the rmsd by using above mentioned files, but I have
> > got nothing.
> >
>
> That's what we have, too. :-) What was your exact command and what did you
> get as output?
>
> Mark
>
> If it is possible to calculate the rmsd from the energy minimized
> > structure, kindly tell me how do we do it.
> >
> > Thanks in advance
> > Surya
> > Graduate student
> > India.
> > --
> > 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: 6
> Date: Mon, 1 Dec 2014 13:55:45 +0530
> From: RINU KHATTRI <nickname.mittu at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] error in PME mesh load
> Message-ID:
> <
> CAOEfx3+yUpLcnM3f0d_znEqDiFSzrB6s9wGX-2X3mG-o3L5MQg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hello gromacs user
> i am working on complex with popc membrane i have problem in minimization
> step
> grompp -f minim1.mdp -c system_inflated.gro -p topol.top -o emr.tpr
> i got these notes how to adjust the load imbalance i red previous
> mails but it doesn't work my minimization file is
> define = -DSTRONG_POSRES
> integrator = steep
> emtol = 1000.0
> emstep = 0.01
> nsteps = 50000
>
> nstlist = 1
> ns_type = grid
> rlist = 1.2
> coulombtype = PME
> rcoulomb = 1.2
> rvdw = 1.2
> pbc = xyz
>
>
> System has non-zero total charge: 13.999998
> Total charge should normally be an integer. See
>
>
> Analysing residue names:
> There are: 408 Protein residues
> There are: 123 Other residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and
> splitting into groups...
> Number of degrees of freedom in T-Coupling group rest is 30828.00
> Largest charge group radii for Van der Waals: 0.252, 0.251 nm
> Largest charge group radii for Coulomb: 0.252, 0.251 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 288x288x128, spacing 0.114 0.114 0.117
> Estimate for the relative computational load of the PME mesh part: 0.99
>
> NOTE 2 [file minim1.mdp]:
> The optimal PME mesh load for parallel simulations is below 0.5
> and for highly parallel simulations between 0.25 and 0.33,
> for higher performance, increase the cut-off and the PME grid spacing
>
> kindly help
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 1 Dec 2014 11:54:05 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] error in PME mesh load
> Message-ID:
> <
> CAMNuMATrafDLXccOxv2rqEH5U0Rpg5EBx_B7+xkeHZPOhq9obA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Performance really doesn't matter for a typical energy minimization.
> Running it probably takes less time than emailing :-)
>
> Mark
>
> On Mon, Dec 1, 2014 at 9:25 AM, RINU KHATTRI <nickname.mittu at gmail.com>
> wrote:
>
> > hello gromacs user
> > i am working on complex with popc membrane i have problem in minimization
> > step
> > grompp -f minim1.mdp -c system_inflated.gro -p topol.top -o emr.tpr
> > i got these notes how to adjust the load imbalance i red previous
> > mails but it doesn't work my minimization file is
> > define = -DSTRONG_POSRES
> > integrator = steep
> > emtol = 1000.0
> > emstep = 0.01
> > nsteps = 50000
> >
> > nstlist = 1
> > ns_type = grid
> > rlist = 1.2
> > coulombtype = PME
> > rcoulomb = 1.2
> > rvdw = 1.2
> > pbc = xyz
> >
> >
> > System has non-zero total charge: 13.999998
> > Total charge should normally be an integer. See
> >
> >
> > Analysing residue names:
> > There are: 408 Protein residues
> > There are: 123 Other residues
> > Analysing Protein...
> > Analysing residues not classified as Protein/DNA/RNA/Water and
> > splitting into groups...
> > Number of degrees of freedom in T-Coupling group rest is 30828.00
> > Largest charge group radii for Van der Waals: 0.252, 0.251 nm
> > Largest charge group radii for Coulomb: 0.252, 0.251 nm
> > Calculating fourier grid dimensions for X Y Z
> > Using a fourier grid of 288x288x128, spacing 0.114 0.114 0.117
> > Estimate for the relative computational load of the PME mesh part: 0.99
> >
> > NOTE 2 [file minim1.mdp]:
> > The optimal PME mesh load for parallel simulations is below 0.5
> > and for highly parallel simulations between 0.25 and 0.33,
> > for higher performance, increase the cut-off and the PME grid spacing
> >
> > kindly help
> > --
> > 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.
> >
>
>
> ------------------------------
>
> --
> 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.
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>
> End of gromacs.org_gmx-users Digest, Vol 128, Issue 1
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