RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again

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

[gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)

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RE: [gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)

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[gmx-users] make-hole

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

[gmx-users] Venkat C has sent you a private message

Title: Private Message from Venkat Venkat C has sent you a private message Click to read messagePlease read it or Venkat will think you ignored this :( This message has been forwarded at the request of venkat...@gmail.com. To block all emails from FanIQ, please click here. FanIQ

Re: [gmx-users] make-hole

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

Re: [gmx-users] how to save grace out put to jpeg or grafifal pic

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 printing

[gmx-users] Gromacs on SPARC

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,

[gmx-users] Re: Free energy with Gromacs.

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

[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

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

[gmx-users] g_rdf program

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

[gmx-users] Re: Free energy with Gromacs.

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

[gmx-users] Help parameterizing ddb to work with vsite -h option of pdb2gmx

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

RE: [gmx-users] g_rdf program

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

[gmx-users] Doubt regarding membrane protein in POPC bilayer

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

[gmx-users] how to get the the force plot after pulling dynamic simulation using GMX-3.3

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)