Dear Gromacs developer:
I am asking for your help about fitting a dihedral angle parameters using
gromacs md simulation. One article (link:
http://www.mpip-mainz.mpg.de/~andrienk/journal_club/opls.pdf) says that
fitting a dihedral angle potential parameters needs three steps: 1)
perform ab initio
Hi
How Potential of Mean Force (PMF) is calculated by gromacs? what command?
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WU Yanbin wrote:
Hi, all,
According to Manual v3.3, "It's possible to apply multiple bonded
interactions of the same type on the same atoms" [12th line of Page 98].
If a dihedral potential for 4 neighboring atoms is defined 3 times using
the "periodic type" in the topology file, like
V=k1*(
leila karami wrote:
Hi
How Potential of Mean Force (PMF) is calculated by gromacs? what command?
Calculating the PMF is not a command, but rather a somewhat extensive simulation
procedure that will depend upon the quantity you want to measure (binding energy
of a ligand, PMF of rotating
Hi all,
I've been working on an umbrella sampling/PMF tutorial for some time now, and I
have just added it to the Tutorials page on the Gromacs site. As with my
previous tutorials, I would welcome anyone to look through it and give me any
feedback you may have on making it better; feel free
I have never done this myself. Nevertheless, I'm going to take a shot
since you haven't got an answer yet.
Dihedral parameters can be thought of as consistently developed fudge
factors that are used to fine-tune a parameter set. The word
consistent here implies that there is a method to dev
Dear Mr. Chris:
Thanks for your reply! I will try your method!
best regards,
fangyong
> I have never done this myself. Nevertheless, I'm going to take a shot
> since you haven't got an answer yet.
>
> Dihedral parameters can be thought of as consistently developed fudge
> factors that are used
Dear Sir,
I energy optimised the polymer-protein structure using HYPERCHEM. The moment I
created peptide bonds between them, the pdb was saved like the format mentioned
previously. for eg;
HETATM1 N 1-24.998 12.703 12.925
>
> HETATM2 C 2-24.749 12.813 11.
Hi,I want to simulate gas adsorption on finite CNT. Does CNT be flexible
or rigid? which is better? thanks
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Please don
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 30
QMlevel: RHF/STO-3G
number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
[yoochancal2-desktop:09740] *** Process received signal ***
[yoochancal2-
On 24/01/10 18:02, P.R.Anand Narayanan wrote:
Dear Sir,
I energy optimised the polymer-protein structure using HYPERCHEM. The
moment I created peptide bonds between them, the pdb was saved like the
format mentioned previously. for eg;
HETATM 1 N 1 -24.998 12.703 12.925
>
> HETATM 2 C 2 -24.749
On 24/01/10 18:16, leila karami wrote:
Hi,I want to simulate gas adsorption on finite CNT. Does CNT be
flexible or rigid? which is better? thanks
... whichever models the real conditions better. The only way we'd know
would be by doing such work or reading about such work. Either way,
you'
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