[gmx-users] totally misunderstood question about genbox
WILLIAM R WELCH
wwelch at wisc.edu
Tue Mar 13 22:58:08 CET 2007
Mark
I'm sorry--that is not what I was saying at all--I did not have ANY waters originally defined in my .top file. I used editconf to make a cubic box that was 6 x 6 x 6 , then used genbox and in that step specified which topology file in which to insert the waters--a .top file with no water. Genbox then ilisted a different number of waters at the end of the .top file than what it had put in the .gro file. I just think it is strange that the program would itself generate two different numbers for the same thing all in one step.
Will
>
> > >
> > Why would genbox put more water molecules in my .gro file than in
> my .top
> > file? I'm sure all I have to do is edit the number in my top file,
> but I
> > have not had this happen before, does anyone know of a reason that
> this
> > happens so I can fix my file?
>
> genbox doesn't read a top and produce that many solvent molecules.
> For a
> start, how does it know what shape you want them in? Read "man genbox",
> choose what you want to do, apply genbox, and then edit your .top so
> the
> number of waters agrees with what genbox produced... not the other way
> around.
>
> Mark
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 08 Mar 2007 12:05:19 +1000
> From: Itamar Kass <ikass at uq.edu.au>
> Subject: [gmx-users] PME, epsilon_rf and dielectric constant
> calculation
> To: Gromax user group <gmx-users at gromacs.org>
> Message-ID: <45EF6F5F.6010704 at uq.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
>
> I wish to calculate the dielectric constant of small molecules liquids.
> In order to do so, I am simulating the system using PME, with
> epsilon_r
> = 1.
>
> I have few questions:
> 1. What is the meaning of epsilon_rf when I am using PME, if it
> important, what it should be?
> 2. Whet is the best way to calculate the dielectric constant of the
> simulation box, does g_dipole is enough or should I use g_dielectric
> also.
>
> Best, Itamar
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 8 Mar 2007 13:17:39 +1100 (EST)
> From: "Mark Abraham" <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] PME, epsilon_rf and dielectric constant
> calculation
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <36119.150.203.145.27.1173320259.squirrel at sqmail.anu.edu.au>
> Content-Type: text/plain;charset=iso-8859-1
>
> > Dear all,
> >
> > I wish to calculate the dielectric constant of small molecules liquids.
> > In order to do so, I am simulating the system using PME, with epsilon_r
> > = 1.
> >
> > I have few questions:
> > 1. What is the meaning of epsilon_rf when I am using PME, if it
> > important, what it should be?
>
> Have you looked in section 7.3?
>
> > 2. Whet is the best way to calculate the dielectric constant of the
> > simulation box, does g_dipole is enough or should I use
> g_dielectric also.
>
> I don't know.
>
> Mark
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 08 Mar 2007 12:28:46 +1000
> From: Itamar Kass <ikass at uq.edu.au>
> Subject: Re: [gmx-users] PME, epsilon_rf and dielectric constant
> calculation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <45EF74DE.8000004 at uq.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Mark,
>
> I read the manual few times looking for a clue. The only thing I
> could
> understand it that epsilon_rf is not taking inti account if I don't
> use
> reaction field.
>
> Best, Itamar.
>
> Mark Abraham wrote:
> >>Dear all,
> >>
> >>I wish to calculate the dielectric constant of small molecules liquids.
> >>In order to do so, I am simulating the system using PME, with epsilon_r
> >> = 1.
> >>
> >>I have few questions:
> >>1. What is the meaning of epsilon_rf when I am using PME, if it
> >>important, what it should be?
> >
> >
> > Have you looked in section 7.3?
> >
> >
> >>2. Whet is the best way to calculate the dielectric constant of the
> >>simulation box, does g_dipole is enough or should I use
> g_dielectric also.
> >
> >
> > I don't know.
> >
> > Mark
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
>
> "Prediction is very difficult, especially about the future" - Niels Bohr
>
> ===========================================
> | Itamar Kass
> | Postdoctoral Research Fellow
> |
> | Molecular Dynamics Group
> | School of Molecular and Microbial Sciences (SMMS)
> | Chemistry Building (#68)
> | The University of Queensland
> | St. Lucia Campus, Brisbane, QLD 4067
> | Australia
> |
> | Tel: +61 7 3346 9922
> | Fax: +61 7 3365 3872
> | email: ikass at uq.edu.au
> ============================================
>
>
> Unless stated otherwise, this e-mail represents only the views of the
>
> Sender and not the views of The University of Queensland
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 8 Mar 2007 13:34:41 +1100 (EST)
> From: "Mark Abraham" <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] PME, epsilon_rf and dielectric constant
> calculation
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <43826.150.203.145.27.1173321281.squirrel at sqmail.anu.edu.au>
> Content-Type: text/plain;charset=iso-8859-1
>
> > Dear Mark,
> >
> > I read the manual few times looking for a clue. The only thing I could
> > understand it that epsilon_rf is not taking inti account if I don't
> use
> > reaction field.
>
> 7.3.9 clearly says "epsilon_rf: (1) The relative dielectric constant
> of
> the reaction field. This is only used with reaction-field electrostatics.
> A value of 0 means infinity."
>
> Mark
>
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 8 Mar 2007 13:17:56 +0800
> From: "kitty ji" <jiqing at iccas.ac.cn>
> Subject: Re: Re: [gmx-users] vacuum right but melt collapse
> To: <gmx-users at gromacs.org>
> Message-ID: <003201c76141$214f4480$8ebbe29f at jiqing>
> Content-Type: text/plain; charset="utf-8"
>
> Tsjerk Wassenaar, thank you very much for you suggestion even if most
> of them have been manipulated.
>
>
>
> "Write out the energies at every step and check which of the energy
> contributions goes astray. This may give you a good clue to where
> you're mistake is. Also, run through the topology again, by hand,
> checking all bonds, angles, dihedrals, exclusion (implicit ones!),
> etc."
>
> when the explosion happened, the energy of bond, angle and potential
> will were increase. And the topology has been checked several times.
>
>
>
>
>
> Now I increase the cutoff of VDW & Coulomb from 0.9 to 1.5. The
> system looks ok from last night to this time. If the problem is fixed,
> I conclude that cutoff 0.9 is not enough for electric system.
>
>
>
> Hope this conclusion is helpful for GMX users.
>
>
>
>
> Message: 2
> Date: Wed, 7 Mar 2007 17:49:30 +0100
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Subject: Re: Re: [gmx-users] vacuum right but melt collapse
> To: "kitty ji" <jiqing at iccas.ac.cn>, "Discussion list for GROMACS
> users" <gmx-users at gromacs.org>
> Message-ID:
> <8ff898150703070849r59cb8a8dr60b894a881fcc331 at mail.gmail.com>
> Content-Type: text/plain; charset=GB2312; format=flowed
>
> Hi Ji Qing,
>
> Write out the energies at every step and check which of the energy
> contributions goes astray. This may give you a good clue to where
> you're mistake is. Also, run through the topology again, by hand,
> checking all bonds, angles, dihedrals, exclusion (implicit ones!),
> etc.
>
> Good luck,
>
> Tsjerk
>
> On 3/7/07, kitty ji <jiqing at iccas.ac.cn> wrote:
> >
> >
> > Thanks Mark.
> > But when one polymer chain was used, non-bonded interaction has
> already been
> > there. Because one chain means C44H156O22.
> > After all, I'd like to try more chains.
> >
> > Message: 1
> > Date: Tue, 06 Mar 2007 17:01:52 +1100
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] vacuum right but melt collapse
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <45ED03D0.6010803 at anu.edu.au>
> > Content-Type: text/plain; charset=GB2312
> >
> > kitty ji wrote:
> > > Hi GMX user:
> > >
> > > A model for Poly(vinyl methyl ether) was built with OPLS force
> field (
> > > all H ).
> > >
> > >
> > >
> > > When the model was run alone (a single chain) in vacuum, anything
> goes ok.
> > >
> > >
> > >
> > > But with 45 chains box, the system will be collapse with a little
> bond
> > > elongates abnormal whatever in NVT or NPT.
> > >
> > >
> > >
> > > The relax time of pressure and temperature were adjust but no helpful.
> > >
> > >
> > >
> > > How can I found some possible reason and then fix it ? Any advise
> will
> > > be appreciated.
> >
> > If an isolated molecule doesn't do anything strange, and two more more
> > do, then you have a problem with inter-molecular interactions, i.e.
> the
> > non-bonded ones. Try with just 2 chains to verify this... and look
> > carefully at the atom types and the non-bonded parameters for them.
> >
> > Mark
> >
> >
> >
> > *************************************************
> > Ji Qing
> > Institute of Chemistry, Chinese Academy of Sciences
> > Tel: 0086-10-62562894 ����82618423
> > *************************************************
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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