[gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 87
Alex
nedomacho at gmail.com
Fri May 15 21:46:30 CEST 2015
Golnaz,
I think you're creating a bit of a mess by replying to the digest. If
you don't mind, please see my answer directly to your specific
question, where I will also quote your message from below.
Alex
GR> Thank you Alex
GR> First of all it is better to say that I am a beginner. I follow two papers
GR> for my project. The authers are ''Tumala'' and ''Samalkorpi'' .
GR> My surfactants are mixture of CTAB and SDS. In these two papers surfactants
GR> were put perpendicular on the graphene sheet. because if I put surfactants
GR> random in the box it will take a alot of time for surfactants to transfer
GR> to the graphene sheet. The simulation method in the papers is GROMACS but
GR> authors did not mention how they loacted surfactants on the graphene sheet.
GR> I have written the link of the papers. I knew that it is not specifically
GR> Gromacs but I would like to know with which software I can make this
GR> change on configuration.
GR> http://pubs.acs.org/doi/abs/10.1021/jp077636y
GR> http://pubs.acs.org/doi/abs/10.1021/jp077678m
GR> On Fri, May 15, 2015 at 7:14 PM, <
GR> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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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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>> 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: 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
>> 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 133, Issue 87
>> ******************************************************
>>
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