[gmx-users] no output from rms
Mark Abraham
mark.j.abraham at gmail.com
Wed Dec 3 00:06:56 CET 2014
On Tue, Dec 2, 2014 at 7:16 AM, Seera Suryanarayana <palusoori at gmail.com>
wrote:
> 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
>
Does gmx check on the .trr file tell you that there's data in it? Does the
terminal output of gmx rms look like it found it?
Mark
>
> Surya
> Graduate student
> India.
>
> On Mon, Dec 1, 2014 at 4:24 PM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users at maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gromacs.org_gmx-users-request at maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> > gromacs.org_gmx-users-owner at maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > 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
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> >
> > End of gromacs.org_gmx-users Digest, Vol 128, Issue 1
> > *****************************************************
> >
>
> --
> 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.
>
>
More information about the gromacs.org_gmx-users
mailing list