[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 1
Victor Rosas Garcia
rosas.victor at gmail.com
Tue Dec 2 23:50:02 CET 2014
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Victor
2014-12-02 0:16 GMT-06:00 Seera Suryanarayana <palusoori at gmail.com>:
> 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
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>>
>> End of gromacs.org_gmx-users Digest, Vol 128, Issue 1
>> *****************************************************
>>
>
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