[gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 2 12:05:46 CET 2010
On 2/11/2010 9:28 PM, Amin Arabbagheri wrote:
>
> Hi Mark,
>
> Are there differences between functions 9 and 1? So can I implement
> these dihedrals in successive lines, just using function 9 or 1?
>
Please read the dihedral manual sections in chapter 4 and 5 and have a
look at (e.g.) some examples in the AMBER FF files.
Mark
>
> Amin
> --- On *Tue, 2/11/10, gmx-users-request at gromacs.org
> /<gmx-users-request at gromacs.org>/* wrote:
>
>
> From: gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> Subject: gmx-users Digest, Vol 79, Issue 8
> To: gmx-users at gromacs.org
> Date: Tuesday, 2 November, 2010, 5:29
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
> </mc/compose?to=gmx-users-request at gromacs.org>
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
> </mc/compose?to=gmx-users-owner at gromacs.org>
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: multiple torsions for one dihedral (Mark Abraham)
> 2. questions about umbrella sampling (mircial at sjtu.edu.cn
> </mc/compose?to=mircial at sjtu.edu.cn>)
> 3. RE: Reg:walls and pbc xy (Berk Hess)
> 4. Re: Reg:walls and pbc xy (vinothkumar mohanakrishnan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 02 Nov 2010 17:21:29 +1100
> From: Mark Abraham <mark.abraham at anu.edu.au
> </mc/compose?to=mark.abraham at anu.edu.au>>
> Subject: Re: [gmx-users] multiple torsions for one dihedral
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>>
> Message-ID: <fbbaf7a444d7e.4cd04899 at anu.edu.au
> </mc/compose?to=fbbaf7a444d7e.4cd04899 at anu.edu.au>>
> Content-Type: text/plain; charset="us-ascii"
>
> Yes, multiple "type 1" dihedrals for use with AMBER and CHARMM
> forcefields can be implemented, either as successive
> [dihedraltypes] of type 9 (since GROMACS 4.0, IIRC) or as multiple
> [dihedrals] of type 1 (since ages).
>
> Mark
>
> ----- Original Message -----
> From: Amin Arabbagheri <amin_arab at yahoo.com
> </mc/compose?to=amin_arab at yahoo.com>>
> Date: Tuesday, November 2, 2010 17:06
> Subject: [gmx-users] multiple torsions for one dihedral
> To: gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>
>
> -----------------------------------------------------------
> | > Hi all,
> >
> > I'm using AMBER99p force field in GROMACS. In the AMBER
> forcefield for some dihedrals, there are several values, in which
> n values are different.
> > As an example, for C3-C3-N-C, I have
> > C3-C3-N-C .50 180.0 -4
> > C3-C3-N-C .15 180.0 -3
> > C3-C3-N-C .53 0.0 1
> >
> > For the version 4, is there a convenient way to use these
> multiple dihedrals?
> > Thanks,
> > Amin
> >
> |
> -----------------------------------------------------------
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> </mc/compose?to=gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/9d1f3ca5/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Tue, 02 Nov 2010 15:16:55 +0800
> From: mircial at sjtu.edu.cn </mc/compose?to=mircial at sjtu.edu.cn>
> Subject: [gmx-users] questions about umbrella sampling
> To: gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>
> Message-ID: <20101102151655.msoayn0bno4gk40k at webmail.sjtu.edu.cn
> </mc/compose?to=20101102151655.msoayn0bno4gk40k at webmail.sjtu.edu.cn>>
> Content-Type: text/plain; charset=GB2312; DelSp="Yes";
> format="flowed"
>
> Dear All:
>
> I am using umbrella sampling method to calculate potential of mean
> force and I encountered the following questions:
> 1, at the *.ppa file, I need to incorporate a parameter indicating the
> "the position of the pull group will restraint to, relative to the
> reference group" (i.e., the "pos1" parameter).
>
> To my understanding, in the initial structure, the pull group is not
> need to at the exact position defined by the aformationed parameter
> ("pos1" parameter) in the .ppa file. I just need to put the pull group
> near that position, am I right?
>
> 2, Since I need to define the position of the pull group relative to
> the reference group. I need to calculate the mass center of the
> reference group as well as that of the pull group. Does there any
> tools in GROMACS to calculate their mass center?
>
> Thank you very much for your time and your kindness!
>
> Best Regards
>
> R-X Gu
>
>
>
> ----- 完成转寄邮件 -----
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 2 Nov 2010 09:07:19 +0100
> From: Berk Hess <gmx3 at hotmail.com </mc/compose?to=gmx3 at hotmail.com>>
> Subject: RE: [gmx-users] Reg:walls and pbc xy
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>>
> Message-ID: <COL113-W21D35D03BE8961C73BD6188E490 at phx.gbl
> </mc/compose?to=COL113-W21D35D03BE8961C73BD6188E490 at phx.gbl>>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> With wall_r_linpot your wall potential is linear from 1 nm downwards.
> Since the LJ force is negative at 1 nm, your atoms are attracted
> to the walls.
>
> But why not simply use two interfaces? You get double the sampling
> for free
> and you do not have to bother with complicated wall setups.
>
> Berk
>
> Date: Tue, 2 Nov 2010 11:49:48 +0530
> From: kmvinoth at gmail.com </mc/compose?to=kmvinoth at gmail.com>
> To: gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>
> Subject: [gmx-users] Reg:walls and pbc xy
>
> Hi Gromacians
>
> I want to create a liquid-liquid interface and study its
> properties. Hence i combined two boxes ( say water and DCE). The
> two boxes are well equilibrated before merging and i created an
> interface. Now i want to perform energy minimisation for the
> interface by appling pbc in the xy direction and using walls. ( If
> i apply pbc in all the directions i get two interfaces where as i
> need only one interface hence i am applying it only on the xy
> direction and removing the boundary condition in the Z
> direction.).When i performed the energy minimisation for the
> interfacial system but i found that my system is exploding
> (several PDB files are written while running mdrun is executed)
> and i dont know why?.There is no issue when i use pbc in all
> directions. below is my em.mdp file. any help is highly appreciated.
>
>
> integrator = steep
> emtol = 40.0
> emstep = 0.01
> nsteps = 10000
> nstxout = 100
> nstvout = 100
> nstfout = 100
> nstlog = 100
>
> nstenergy = 100
> nstlist = 5
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = Cut-off
> rvdw = 1.0
>
> ewald_geometry = 3dc
> nwall = 2
> wall_type = 9-3
> wall_r_linpot = 1
> wall_atomtype = opls_966 opls_968
> wall_density = 9-3 9-3
> wall_ewald_zfac = 3
> pbc = xy
> fourierspacing = 0.18
>
>
>
> Regards
> Vinoth
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> </mc/compose?to=gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/2914ee6c/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Tue, 2 Nov 2010 14:59:31 +0530
> From: vinothkumar mohanakrishnan <kmvinoth at gmail.com
> </mc/compose?to=kmvinoth at gmail.com>>
> Subject: Re: [gmx-users] Reg:walls and pbc xy
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>>
> Message-ID:
> <AANLkTi=rKZv+4nmS0O5htkMLZ4nr0yaWLARCH2VWgd6i at mail.gmail.com
> </mc/compose?to=4nmS0O5htkMLZ4nr0yaWLARCH2VWgd6i at mail.gmail.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Berk
>
> I need only one interface because if i have two interfaces the
> "capillary
> waves from one interface disturb the other even though the
> distance between
> the average positions of the two interfaces are larger than the
> potential
> cut-off" (this was said in the literature).
>
> Can anyone explain me why walls are used for interfaces? and what
> is the
> purpose of using walls?.
> suppose if i put nwall =2 where exactly are the walls created? can
> anyone
> explain me with an example?
>
> i read the manual but it is not making any sense to me. if i know
> this i
> know what correction i should make in my mdp file to make it work
> for pbc
> xy. any help is highly appreciated.
>
> Regards
> Vinoth
>
> On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess <gmx3 at hotmail.com
> </mc/compose?to=gmx3 at hotmail.com>> wrote:
>
> > Hi,
> >
> > With wall_r_linpot your wall potential is linear from 1 nm
> downwards.
> > Since the LJ force is negative at 1 nm, your atoms are attracted
> to the
> > walls.
> >
> > But why not simply use two interfaces? You get double the
> sampling for free
> > and you do not have to bother with complicated wall setups.
> >
> > Berk
> >
> > ------------------------------
> > Date: Tue, 2 Nov 2010 11:49:48 +0530
> > From: kmvinoth at gmail.com </mc/compose?to=kmvinoth at gmail.com>
> > To: gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>
> > Subject: [gmx-users] Reg:walls and pbc xy
> >
> >
> > Hi Gromacians
> >
> > I want to create a liquid-liquid interface and study its
> properties. Hence
> > i combined two boxes ( say water and DCE). The two boxes are well
> > equilibrated before merging and i created an interface. Now i
> want to
> > perform energy minimisation for the interface by appling pbc in
> the xy
> > direction and using walls. ( If i apply pbc in all the
> directions i get two
> > interfaces where as i need only one interface hence i am
> applying it only on
> > the xy direction and removing the boundary condition in the Z
> > direction.).When i performed the energy minimisation for the
> interfacial
> > system but i found that my system is exploding (several PDB
> files are
> > written while running mdrun is executed) and i dont know
> why?.There is no
> > issue when i use pbc in all directions. below is my em.mdp file.
> any help is
> > highly appreciated.
> >
> > integrator = steep
> > emtol = 40.0
> > emstep = 0.01
> > nsteps = 10000
> > nstxout = 100
> > nstvout = 100
> > nstfout = 100
> > nstlog = 100
> > nstenergy = 100
> > nstlist = 5
> > ns_type = grid
> > rlist = 1.0
> > coulombtype = PME
> > rcoulomb = 1.0
> > vdwtype = Cut-off
> > rvdw = 1.0
> > ewald_geometry = 3dc
> > nwall = 2
> > wall_type = 9-3
> > wall_r_linpot = 1
> > wall_atomtype = opls_966 opls_968
> > wall_density = 9-3 9-3
> > wall_ewald_zfac = 3
> > pbc = xy
> > fourierspacing = 0.18
> >
> >
> > Regards
> > Vinoth
> >
> > -- gmx-users mailing list gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users Please
> search the
> > archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> before
> > posting! Please don't post (un)subscribe requests to the list.
> Use the www
> > interface or send it to gmx-users-request at gromacs.org
> </mc/compose?to=gmx-users-request at gromacs.org>. Can't post? Read
> > http://www.gromacs.org/Support/Mailing_Lists
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> </mc/compose?to=gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/7fffaaa1/attachment.html
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 79, Issue 8
> ****************************************
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101102/1d16084e/attachment.html>
More information about the gromacs.org_gmx-users
mailing list