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On 2/11/2010 9:28 PM, Amin Arabbagheri wrote:
<blockquote cite="mid:616245.27387.qm@web114716.mail.gq1.yahoo.com"
type="cite">
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Hi Mark,<br>
<br>
Are there differences between functions 9 and 1? So can I
implement these dihedrals in successive lines, just using
function 9 or 1?<br>
</td>
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</blockquote>
<br>
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.<br>
<br>
Mark<br>
<blockquote cite="mid:616245.27387.qm@web114716.mail.gq1.yahoo.com"
type="cite">
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Amin<br>
--- On <b>Tue, 2/11/10, <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <i><a class="moz-txt-link-rfc2396E" href="mailto:gmx-users-request@gromacs.org"><gmx-users-request@gromacs.org></a></i></b>
wrote:<br>
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From: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users-request@gromacs.org"><gmx-users-request@gromacs.org></a><br>
Subject: gmx-users Digest, Vol 79, Issue 8<br>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Date: Tuesday, 2 November, 2010, 5:29<br>
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Today's Topics:<br>
<br>
1. Re: multiple torsions for one dihedral (Mark
Abraham)<br>
2. questions about umbrella sampling (<a
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ymailto="mailto:mircial@sjtu.edu.cn"
href="/mc/compose?to=mircial@sjtu.edu.cn">mircial@sjtu.edu.cn</a>)<br>
3. RE: Reg:walls and pbc xy (Berk Hess)<br>
4. Re: Reg:walls and pbc xy (vinothkumar
mohanakrishnan)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 02 Nov 2010 17:21:29 +1100<br>
From: Mark Abraham <<a moz-do-not-send="true"
ymailto="mailto:mark.abraham@anu.edu.au"
href="/mc/compose?to=mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] multiple torsions for one
dihedral<br>
To: Discussion list for GROMACS users <<a
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<br>
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).<br>
<br>
Mark<br>
<br>
----- Original Message -----<br>
From: Amin Arabbagheri <<a moz-do-not-send="true"
ymailto="mailto:amin_arab@yahoo.com"
href="/mc/compose?to=amin_arab@yahoo.com">amin_arab@yahoo.com</a>><br>
Date: Tuesday, November 2, 2010 17:06<br>
Subject: [gmx-users] multiple torsions for one
dihedral<br>
To: <a moz-do-not-send="true"
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href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
-----------------------------------------------------------<br>
| > Hi all,<br>
> <br>
> 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. <br>
> As an example, for C3-C3-N-C, I have<br>
> C3-C3-N-C .50 180.0 -4<br>
> C3-C3-N-C .15 180.0 -3<br>
> C3-C3-N-C .53 0.0 1<br>
> <br>
> For the version 4, is there a convenient way to
use these multiple dihedrals?<br>
> Thanks,<br>
> Amin<br>
> <br>
|<br>
-----------------------------------------------------------<br>
> <br>
> -- <br>
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Message: 2<br>
Date: Tue, 02 Nov 2010 15:16:55 +0800<br>
From: <a moz-do-not-send="true"
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Subject: [gmx-users] questions about umbrella sampling<br>
To: <a moz-do-not-send="true"
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<br>
Dear All:<br>
<br>
I am using umbrella sampling method to calculate
potential of mean<br>
force and I encountered the following questions:<br>
1, at the *.ppa file, I need to incorporate a
parameter indicating the<br>
"the position of the pull group will restraint to,
relative to the<br>
reference group" (i.e., the "pos1" parameter).<br>
<br>
To my understanding, in the initial structure, the
pull group is not<br>
need to at the exact position defined by the
aformationed parameter<br>
("pos1" parameter) in the .ppa file. I just need to
put the pull group<br>
near that position, am I right?<br>
<br>
2, Since I need to define the position of the pull
group relative to<br>
the reference group. I need to calculate the mass
center of the<br>
reference group as well as that of the pull group.
Does there any<br>
tools in GROMACS to calculate their mass center?<br>
<br>
Thank you very much for your time and your kindness!<br>
<br>
Best Regards<br>
<br>
R-X Gu<br>
<br>
<br>
<br>
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<br>
Message: 3<br>
Date: Tue, 2 Nov 2010 09:07:19 +0100<br>
From: Berk Hess <<a moz-do-not-send="true"
ymailto="mailto:gmx3@hotmail.com"
href="/mc/compose?to=gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] Reg:walls and pbc xy<br>
To: Discussion list for GROMACS users <<a
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<br>
<br>
Hi,<br>
<br>
With wall_r_linpot your wall potential is linear from
1 nm downwards.<br>
Since the LJ force is negative at 1 nm, your atoms are
attracted to the walls.<br>
<br>
But why not simply use two interfaces? You get double
the sampling for free<br>
and you do not have to bother with complicated wall
setups.<br>
<br>
Berk<br>
<br>
Date: Tue, 2 Nov 2010 11:49:48 +0530<br>
From: <a moz-do-not-send="true"
ymailto="mailto:kmvinoth@gmail.com"
href="/mc/compose?to=kmvinoth@gmail.com">kmvinoth@gmail.com</a><br>
To: <a moz-do-not-send="true"
ymailto="mailto:gmx-users@gromacs.org"
href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Reg:walls and pbc xy<br>
<br>
Hi Gromacians<br>
<br>
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.<br>
<br>
<br>
integrator = steep <br>
emtol = 40.0 <br>
emstep = 0.01<br>
nsteps = 10000 <br>
nstxout = 100 <br>
nstvout = 100 <br>
nstfout = 100 <br>
nstlog = 100 <br>
<br>
nstenergy = 100 <br>
nstlist = 5 <br>
ns_type = grid <br>
rlist = 1.0 <br>
coulombtype = PME <br>
rcoulomb = 1.0 <br>
vdwtype = Cut-off <br>
rvdw = 1.0 <br>
<br>
ewald_geometry = 3dc<br>
nwall = 2<br>
wall_type = 9-3<br>
wall_r_linpot = 1<br>
wall_atomtype = opls_966 opls_968<br>
wall_density = 9-3 9-3<br>
wall_ewald_zfac = 3<br>
pbc = xy <br>
fourierspacing = 0.18 <br>
<br>
<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
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Message: 4<br>
Date: Tue, 2 Nov 2010 14:59:31 +0530<br>
From: vinothkumar mohanakrishnan <<a
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Subject: Re: [gmx-users] Reg:walls and pbc xy<br>
To: Discussion list for GROMACS users <<a
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<br>
Hi Berk<br>
<br>
I need only one interface because if i have two
interfaces the "capillary<br>
waves from one interface disturb the other even though
the distance between<br>
the average positions of the two interfaces are larger
than the potential<br>
cut-off" (this was said in the literature).<br>
<br>
Can anyone explain me why walls are used for
interfaces? and what is the<br>
purpose of using walls?.<br>
suppose if i put nwall =2 where exactly are the walls
created? can anyone<br>
explain me with an example?<br>
<br>
i read the manual but it is not making any sense to
me. if i know this i<br>
know what correction i should make in my mdp file to
make it work for pbc<br>
xy. any help is highly appreciated.<br>
<br>
Regards<br>
Vinoth<br>
<br>
On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess <<a
moz-do-not-send="true"
ymailto="mailto:gmx3@hotmail.com"
href="/mc/compose?to=gmx3@hotmail.com">gmx3@hotmail.com</a>>
wrote:<br>
<br>
> Hi,<br>
><br>
> With wall_r_linpot your wall potential is linear
from 1 nm downwards.<br>
> Since the LJ force is negative at 1 nm, your
atoms are attracted to the<br>
> walls.<br>
><br>
> But why not simply use two interfaces? You get
double the sampling for free<br>
> and you do not have to bother with complicated
wall setups.<br>
><br>
> Berk<br>
><br>
> ------------------------------<br>
> Date: Tue, 2 Nov 2010 11:49:48 +0530<br>
> From: <a moz-do-not-send="true"
ymailto="mailto:kmvinoth@gmail.com"
href="/mc/compose?to=kmvinoth@gmail.com">kmvinoth@gmail.com</a><br>
> To: <a moz-do-not-send="true"
ymailto="mailto:gmx-users@gromacs.org"
href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: [gmx-users] Reg:walls and pbc xy<br>
><br>
><br>
> Hi Gromacians<br>
><br>
> I want to create a liquid-liquid interface and
study its properties. Hence<br>
> i combined two boxes ( say water and DCE). The
two boxes are well<br>
> equilibrated before merging and i created an
interface. Now i want to<br>
> perform energy minimisation for the interface by
appling pbc in the xy<br>
> direction and using walls. ( If i apply pbc in
all the directions i get two<br>
> interfaces where as i need only one interface
hence i am applying it only on<br>
> the xy direction and removing the boundary
condition in the Z<br>
> direction.).When i performed the energy
minimisation for the interfacial<br>
> system but i found that my system is exploding
(several PDB files are<br>
> written while running mdrun is executed) and i
dont know why?.There is no<br>
> issue when i use pbc in all directions. below is
my em.mdp file. any help is<br>
> highly appreciated.<br>
><br>
> integrator = steep<br>
> emtol = 40.0<br>
> emstep = 0.01<br>
> nsteps = 10000<br>
> nstxout = 100<br>
> nstvout = 100<br>
> nstfout = 100<br>
> nstlog = 100<br>
> nstenergy = 100<br>
> nstlist = 5<br>
> ns_type = grid<br>
> rlist = 1.0<br>
> coulombtype = PME<br>
> rcoulomb = 1.0<br>
> vdwtype = Cut-off<br>
> rvdw = 1.0<br>
> ewald_geometry = 3dc<br>
> nwall = 2<br>
> wall_type = 9-3<br>
> wall_r_linpot = 1<br>
> wall_atomtype = opls_966 opls_968<br>
> wall_density = 9-3 9-3<br>
> wall_ewald_zfac = 3<br>
> pbc = xy<br>
> fourierspacing = 0.18<br>
><br>
><br>
> Regards<br>
> Vinoth<br>
><br>
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href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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Please search the archive at <a
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before posting!<br>
<br>
End of gmx-users Digest, Vol 79, Issue 8<br>
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