I am recently doing a SMD. I think i did it very well. But i don't know how
to get the force plot. Is there some one can give me a suggestion?
Thank you very much.
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
Sh
Dear gmx-users,
Greetings from Pawan.
I have modelled the structure of a protein using Modeller and then energy
minimized using gromacs.
Then I used the popc128a bilayer from Tieleman sir's website for inserting
the protein.
I created a bigger bilayer using the genconf command in gromacs.
I was ab
No, the molecule has not gone out the side of the box and not entered
the other side. If you check the solvent on the opposite side of the
box, you will notice that there is a big hole that exactly matches up
with the DNA fragment that is sticking out. Use the pbc options in VMD
to display neighb
Hi All,
I am trying to get pdb2gmx -vsite h to work for a sugar attached to my
protein. I am using non standard atom names to differntiate from the OPLS
atom names. I have gone through the manual a few times and I don't
understand the relationship between the files. The ffoplsaa.ddb has bonds
betw
Again, *please keep all Gromacs-related correspondence on the mailing list* The
type of information that you have posted is important to share with others who
may know how to help. I do not know the answer to your problem. I would
suggest contacting the list again with the following informa
Hello, I am relatively new to gromacs and I really would appreciate help with
the following question.
I have used a coarse-grained model to represent a DNA fragment with
approximately 50 nm of length. I have run a Langevin dynamics simulation of DNA
with ions NA+ and CL- to study their distr
Hello,
Searching first the gromacs mailing list I could not find an answer to the
problem I face.
I would like to know the vaules I have to give to the mdp file where it asks
for compressibility.
I have to conduct an NPT simulation using barostat Parrinello-Rahman. My
pressure coupling should
Eudes Fileti wrote:
Hello Justin,
I am facing a very similar problem to that you experienced and described
in (http://www.gromacs.org/pipermail/gmx-users/2008-February/032429.html).
I throw this question in the GMX forum and Berk has kindly helped me.
But reading the forum I realized that y
Dear All,
We are thinking of buying a SPARC T1/T2 cluster with Solaris
as an operating system.
I am therefore wondering if anyone could share his/her experience
of running Gromacs on such (or similar) architecture.
I would appreciate any relevant information (known installation problems,
perform
Homa Azizian wrote:
> hi
> my ques. dose not exactly relate to the gromacs while it is about how I can
> save the resulting plot from grace in to the jpeg or other picture file.
> thanks
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
>
>
One also gets pretty results when first p
Urszula Uciechowska wrote:
Dear users,
I am new to gromacs. I want to make a hole in center of lipid bilayer. My first question is... How can I
get the cx,cy and r values? Its not clear in the manual, and also lipat P8 how to know if its not lipat P6
etc. and what is lipid DMPC ?
Your q
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Dear users,
I am new to gromacs. I want to make a hole in center of lipid bilayer. My first
question is... How can I
get the cx,cy and r values? Its not clear in the manual, and also lipat P8 how
to know if its not lipat P6
etc. and what is lipid DMPC ?
Thanks in advance for any help
Best
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BC
> Rua Santa Adélia, 166 - Bloco B, Sala 1048
> 09210-170 Santo André - SP Brasil
> +55.11.4437-8408
> skype: eefileti
> http://cromo.ufabc.edu.br/~fileti/
> ___
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade F
Hi,
The shape of the dgdl curves also depends a lot on alpha (and sc-sigma).
>From your plots I am guessing that you are doing LJ and electrostatics
at the same time. This always results in high peaks when you have hydrogen
bonding.
Things go much smoother when you first introduce the LJ interac
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