[gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 87
Golnaz Roudsari
golnaz.chem at gmail.com
Fri May 15 21:16:46 CEST 2015
Thank you Alex
First of all it is better to say that I am a beginner. I follow two papers
for my project. The authers are ''Tumala'' and ''Samalkorpi'' .
My surfactants are mixture of CTAB and SDS. In these two papers surfactants
were put perpendicular on the graphene sheet. because if I put surfactants
random in the box it will take a alot of time for surfactants to transfer
to the graphene sheet. The simulation method in the papers is GROMACS but
authors did not mention how they loacted surfactants on the graphene sheet.
I have written the link of the papers. I knew that it is not specifically
Gromacs but I would like to know with which software I can make this
change on configuration.
http://pubs.acs.org/doi/abs/10.1021/jp077636y
http://pubs.acs.org/doi/abs/10.1021/jp077678m
On Fri, May 15, 2015 at 7:14 PM, <
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> Today's Topics:
>
> 1. Re: energy minimization problem (Ming Tang)
> 2. Re: energy minimization problem (Justin Lemkul)
> 3. question (Golnaz Roudsari)
> 4. Re: question (Alex)
> 5. Re: question (abhijit Kayal)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 15 May 2015 13:32:04 +0000
> From: Ming Tang <m21.tang at qut.edu.au>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] energy minimization problem
> Message-ID: <dv888t2enjj742h6jn4fglmx.1431696517727 at email.android.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be
> reasonable according to gromacs website. So ijust kept trying 0.02ps
>
> Sent from my Huawei Mobile
>
> Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 5/14/15 10:02 PM, Ming Tang wrote:
> > Hi Justin
> >
> > Here is the .mdp file with position restraints, which I downloaded from
> the martini tutorial website. It works well with the tutorial and my small
> triple helix, and the grompp process does not give any warnings. Please
> help to have a look. Many thanks to you.
> >
> > define = -DPOSRES
> > integrator = md
> > dt = 0.02
>
> Have you tried simply reducing the time step? 20 fs may be reasonable for
> a
> well equilibrated system, but if the run is dying early, then this is the
> first
> thing I would look at.
>
> -Justin
>
> > nsteps = 50000
> > nstxout = 0
> > nstvout = 0
> > nstlog = 1000
> > nstxtcout = 1000
> > xtc-precision = 10
> > cutoff-scheme =verlet
> > coulombtype = reaction-field-zero
> > coulomb-modifier = potential-shift-verlet
> > rcoulomb-switch = 0.9
> > rcoulomb = 1.4
> > epsilon_r = 15
> > vdw-modifier = force-switch
> > rvdw-switch = 0.9
> > rvdw = 1.4
> > tcoupl = v-rescale
> > tc-grps = Protein W
> > tau-t = 1.0 1.0
> > ref-t = 310 310
> > compressibility = 3e-4
> > ref-p = 1.0
> > refcoord_scaling = all
> > pbc = xyz
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
> Lemkul
> > Sent: Friday, 15 May 2015 11:50 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] energy minimization problem
> >
> >
> >
> > On 5/14/15 9:47 PM, Ming Tang wrote:
> >> Dear Justin,
> >>
> >> I saw it in the terminal.
> >>
> >> Potential Energy = -6.3682131e+05
> >> Maximum force = 1.8876091e+02 on atom 1147
> >> Norm of force = 3.1155257e+00
> >>
> >> But, how can I further minimize my protein?
> >>
> >
> > Minimization is not your problem. Post a full .mdp file of the run that
> is failing.
> >
> > -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
> >
> > ==================================================
> > --
> > 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
>
> ==================================================
> --
> 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: 2
> Date: Fri, 15 May 2015 09:37:44 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] energy minimization problem
> Message-ID: <5555F6A8.7080501 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/15/15 9:32 AM, Ming Tang wrote:
> > Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be
> reasonable according to gromacs website. So ijust kept trying 0.02ps
> >
>
> The time step will depend on the stability of the system, which in turn
> depends
> on how well equilibrated it is. If reducing the time step promotes
> stability
> during equilibration, that is the most obvious solution. After
> equilibrating
> for a while, try increasing the time step.
>
> -Justin
>
> > Sent from my Huawei Mobile
> >
> > Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 5/14/15 10:02 PM, Ming Tang wrote:
> >> Hi Justin
> >>
> >> Here is the .mdp file with position restraints, which I downloaded from
> the martini tutorial website. It works well with the tutorial and my small
> triple helix, and the grompp process does not give any warnings. Please
> help to have a look. Many thanks to you.
> >>
> >> define = -DPOSRES
> >> integrator = md
> >> dt = 0.02
> >
> > Have you tried simply reducing the time step? 20 fs may be reasonable
> for a
> > well equilibrated system, but if the run is dying early, then this is
> the first
> > thing I would look at.
> >
> > -Justin
> >
> >> nsteps = 50000
> >> nstxout = 0
> >> nstvout = 0
> >> nstlog = 1000
> >> nstxtcout = 1000
> >> xtc-precision = 10
> >> cutoff-scheme =verlet
> >> coulombtype = reaction-field-zero
> >> coulomb-modifier = potential-shift-verlet
> >> rcoulomb-switch = 0.9
> >> rcoulomb = 1.4
> >> epsilon_r = 15
> >> vdw-modifier = force-switch
> >> rvdw-switch = 0.9
> >> rvdw = 1.4
> >> tcoupl = v-rescale
> >> tc-grps = Protein W
> >> tau-t = 1.0 1.0
> >> ref-t = 310 310
> >> compressibility = 3e-4
> >> ref-p = 1.0
> >> refcoord_scaling = all
> >> pbc = xyz
> >>
> >> -----Original Message-----
> >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
> Lemkul
> >> Sent: Friday, 15 May 2015 11:50 AM
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] energy minimization problem
> >>
> >>
> >>
> >> On 5/14/15 9:47 PM, Ming Tang wrote:
> >>> Dear Justin,
> >>>
> >>> I saw it in the terminal.
> >>>
> >>> Potential Energy = -6.3682131e+05
> >>> Maximum force = 1.8876091e+02 on atom 1147
> >>> Norm of force = 3.1155257e+00
> >>>
> >>> But, how can I further minimize my protein?
> >>>
> >>
> >> Minimization is not your problem. Post a full .mdp file of the run
> that is failing.
> >>
> >> -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
> >>
> >> ==================================================
> >> --
> >> 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
> >
> > ==================================================
> > --
> > 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: Fri, 15 May 2015 18:46:55 +0430
> From: Golnaz Roudsari <golnaz.chem at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] question
> Message-ID:
> <CAGFO7SEwhXuLkkt=
> 3nWKnh2S8vnUzYVq8jhAtz_r3vQGCYrRTg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gmx-user
> I want to simulate graphene and surfactants in water. In most of the paper
> they put surfactants perpendicular on the graphene sheet. I have problem in
> initial configuration. I do not know how They put them perpendicular on the
> graphene sheet. I can not put them random in my box because I do not have a
> perfect system for more than 50 ns MD run.
> Thank you in advance
> Golnaz Vahabpour
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 15 May 2015 08:26:44 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] question
> Message-ID:
> <CAMJZ6qHMQ2twVjbYXr5P2SL7GyKeTYXfm_HW7DXristSibSL=
> w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I am not sure anyone will be able to help, because this isn't really about
> Gromacs. Can you please clarify who "they" are and what exactly you mean by
> "perpendicular" when talking about surfactants? Also, what are those
> surfactants? Anyway, a reference to a representative paper and some
> instructions on where to quickly see what you're talking about would be
> nice. Once again, this isn't something Gromacs-specific.
>
> Alex
> On May 15, 2015 9:17 AM, "Golnaz Roudsari" <golnaz.chem at gmail.com> wrote:
>
> > Dear gmx-user
> > I want to simulate graphene and surfactants in water. In most of the
> paper
> > they put surfactants perpendicular on the graphene sheet. I have problem
> in
> > initial configuration. I do not know how They put them perpendicular on
> the
> > graphene sheet. I can not put them random in my box because I do not
> have a
> > perfect system for more than 50 ns MD run.
> > Thank you in advance
> > Golnaz Vahabpour
> > --
> > 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: 5
> Date: Fri, 15 May 2015 20:14:18 +0530
> From: abhijit Kayal <abhijitchemiitd at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] question
> Message-ID:
> <CANu9SWi3z=
> UOy12pqSMwPbscMYT7-tXB8ox1CwDkCVVkbh8mmg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> You can use packmol to generate your initial configuration.
>
>
> On Fri, May 15, 2015 at 7:56 PM, Alex <nedomacho at gmail.com> wrote:
>
> > Hi,
> >
> > I am not sure anyone will be able to help, because this isn't really
> about
> > Gromacs. Can you please clarify who "they" are and what exactly you mean
> by
> > "perpendicular" when talking about surfactants? Also, what are those
> > surfactants? Anyway, a reference to a representative paper and some
> > instructions on where to quickly see what you're talking about would be
> > nice. Once again, this isn't something Gromacs-specific.
> >
> > Alex
> > On May 15, 2015 9:17 AM, "Golnaz Roudsari" <golnaz.chem at gmail.com>
> wrote:
> >
> > > Dear gmx-user
> > > I want to simulate graphene and surfactants in water. In most of the
> > paper
> > > they put surfactants perpendicular on the graphene sheet. I have
> problem
> > in
> > > initial configuration. I do not know how They put them perpendicular on
> > the
> > > graphene sheet. I can not put them random in my box because I do not
> > have a
> > > perfect system for more than 50 ns MD run.
> > > Thank you in advance
> > > Golnaz Vahabpour
> > > --
> > > 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.
> >
>
>
>
> --
> Abhijit kayal
> Research Scholar
> Theoretical Chemistry
> IIT Kanpur
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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> End of gromacs.org_gmx-users Digest, Vol 133, Issue 87
> ******************************************************
>
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