[gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8
Amin Arabbagheri
amin_arab at yahoo.com
Tue Nov 2 11:28:24 CET 2010
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?
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
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Today's Topics:
1. Re: multiple torsions for one dihedral (Mark Abraham)
2. questions about umbrella sampling (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>
Subject: Re: [gmx-users] multiple torsions for one dihedral
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <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>
Date: Tuesday, November 2, 2010 17:06
Subject: [gmx-users] multiple torsions for one dihedral
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
>
|
-----------------------------------------------------------
>
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Message: 2
Date: Tue, 02 Nov 2010 15:16:55 +0800
From: mircial at sjtu.edu.cn
Subject: [gmx-users] questions about umbrella sampling
To: gmx-users at gromacs.org
Message-ID: <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 -----
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Message: 3
Date: Tue, 2 Nov 2010 09:07:19 +0100
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] Reg:walls and pbc xy
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <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
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
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Message: 4
Date: Tue, 2 Nov 2010 14:59:31 +0530
From: vinothkumar mohanakrishnan <kmvinoth at gmail.com>
Subject: Re: [gmx-users] Reg:walls and pbc xy
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<AANLkTi=rKZv+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> 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
> 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
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