Hi dear
I think it has got 0.5 in equation.
U=0.5*K(r-b)2
but I dont knoe how do I get K please help me
dtmirij <[EMAIL PROTECTED]> wrote: Hello everyone,
I would like to know does the harmonic biasing potential for running
umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term
incor
Hello everyone,
I would like to know does the harmonic biasing potential for running
umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term
incorporated into the force constant value that we specify?
On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2.
Thank you in advance
Hi all,
I want to simulate a monoclinic crystal with a=0.52 nm, b=1.1 nm, c=2.1
nm and alpha=gama=0, beta=95.6 degree, so I construct a triclinic box. When
I do a NPT simulation, I need the 6 components of compressibility as xx, yy,
zz, xy, xz, yz, according to the manual. I have already get the
In our experience the leaflets of a bilayer have a tendency to
separate if the cutoff on the van der Waals force is too short. We
always use 18-20 angstroms for that.
At 05:35 AM 12/16/2007, you wrote:
pragya chohan wrote:
i started with the lipid coordinates from peter tieleman and
removed
npt, but permit the box to change dimensions independently in the
three directions in response to that component of the virial.
At 11:43 AM 12/16/2007, you wrote:
Dear User
I am starting a membrane simulation. Is it advisablr to complete all
runs in npt or nvt?
Pragya Chohan
--
Det
Hi All,
I am trying to build a bilayer using packmol. The composition is
BTMAC, Stearyl alcohol and water. I am using ffCADMOL force-field. By
packmol when I am trying to build the bilayer initial structure, the
molecules are not straight, but BTMAC and stearyl alcohol are in
zig-zag fashion. I t
Dear User
I am starting a membrane simulation. Is it advisablr to complete all runs in
npt or nvt?
Pragya Chohan
_
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Quoting Xavier Periole <[EMAIL PROTECTED]>:
>
> You do not want to couple the whole system to one bath. Due to the
> exchange of kinetic energy between water and protein you'll end up
> with a frozen protein and warm water.
>
> This is simply due to the different behavior of the water and the
> pr
pragya chohan wrote:
i started with the lipid coordinates from peter tieleman and removed the
water. then i added water by genbox.
I did energy minimization followed by position restrain, which I removed
gradually. all of it was done under npt. I carried out npt for 250
ps. During the next 25
On Sat, 15 Dec 2007 21:58:37 -0500
"Justin A. Lemkul" <[EMAIL PROTECTED]> wrote:
Quoting pragya chohan <[EMAIL PROTECTED]>:
Dear Users
I have a system in of protein with in bound chlorine ion. I also added Na
ion
to the system to neutralize charge on system. I have to couple the system to
w
Behnoush Zare wrote:
Dear Mark,
Sorry about that mistake, the popc.itp file is began with these 3 lines:
;[ moleculetype ]
This is a comment before a directive that tells grompp that this is
going to be a new molecule type. Hence, it thinks it's in the old one,
and that this should be part o
thanks its done. Please read my mail on problem with npt.> Date: Sun, 16 Dec
2007 21:50:33 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org>
Subject: Re: [gmx-users] coupling to water bath> > pragya chohan wrote:> > how
can we do that?> > The same way you make any index file - see >
h
pragya chohan wrote:
how can we do that?
The same way you make any index file - see
http://wiki.gromacs.org/index.php/Index_File
Mark
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Please searc
how can we do that?> Date: Sun, 16 Dec 2007 19:55:30 +1100> From: [EMAIL
PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] coupling to
water bath> > pragya chohan wrote:> > Dear Users> > I have a system in of
protein with in bound chlorine ion. I also added > > Na ion to the syste
Dear Mark,
Sorry about that mistake, the popc.itp file is began with these 3 lines:
;[ moleculetype ]
; Name nrexcl
POPC 3
the error is:
ERROR 1 [file "popc.itp", line 3]:
Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)
Fatal error:
Bonded/nonbonded atom type '1' not fou
Behnoush Zare wrote:
Thanks Yanzi,Thanks Mark,
for your very usefull points,
I have another pdb2gmx running on thr protein.pdb with ffgmx force
filed(matching with lipid.itp).
Also I have removed the including ffG43a1 from the lipid.itp and then running
grompp. The new errors are:
ERROR 1 [fi
Thanks Yanzi,Thanks Mark,
for your very usefull points,
I have another pdb2gmx running on thr protein.pdb with ffgmx force
filed(matching with lipid.itp).
Also I have removed the including ffG43a1 from the lipid.itp and then running
grompp. The new errors are:
ERROR 1 [file "popc.itp", line 3]:
pragya chohan wrote:
Dear Users
I have a system in of protein with in bound chlorine ion. I also added
Na ion to the system to neutralize charge on system. I have to couple
the system to water bath. can i couple protein chlorine and Na together
and solvent separately? or should i couple protei
Farzad Molani wrote:
Hi dear
I want to compute PMF between two amine molecoules by umbrella sampling
but I do'nt know Kn and Posn in umbrella samplig how are determining.
if you are having points please help me.
It sounds like you need some textbook-type material. Try googling
"umbrella samp
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