Re: [gmx-users] [help]How to produce .top file from Material Studio

Hi, I run my simulations in Gromacs but I generated my structure in Materials Studio as well and I agree with Yang Ye - MS will not give you the .top. It`s either x2top or by hand if your system is quite simple or if you can create a topology of one molecule which then can be multiplied wi

Re: [gmx-users] [help]How to produce .top file from Material Studio

No way from MS. Check x2top. Yang YE On Mon, Mar 22, 2010 at 10:42 PM, 程迪 wrote: > Hi,everyone > > I have build a SiO2 structure in Material Studio, And I've set the xyz > coordinates and force field parameters of the structure. Is there some tool > or method to produce a .top file from MS. I d

Re: [gmx-users] Literature for DNA Binding Protein Simulations

Arden Perkins wrote: Dear GROMACS users, I am interested in running a simulation of a DNA-binding peptide and a short stretch of DNA for an undergraduate research project. The pdb file we will be using is a modified version of the Hickman et. al (2004) Rep structure http://www.pdb.org/pdb/ex

[gmx-users] Literature for DNA Binding Protein Simulations

Dear GROMACS users, I am interested in running a simulation of a DNA-binding peptide and a short stretch of DNA for an undergraduate research project. The pdb file we will be using is a modified version of the Hickman et. al (2004) Rep structure http://www.pdb.org/pdb/explore/explore.do?structureId

Re: [gmx-users] Facing difficulty to install gromacs -reg

ITHAYARAJA wrote: Dear sir, I have facing problem with installation on windows xp. could you do clear understanding of it? the problem is, I installed cygwin, unpacking and installation of fftw and gromacs is trouble still I follow the instruction of the same. kindly do your best...

[gmx-users] Facing difficulty to install gromacs -reg

Dear sir, I have facing problem with installation on windows xp. could you do clear understanding of it? the problem is, I installed cygwin, unpacking and installation of fftw and gromacs is trouble still I follow the instruction of the same. kindly do your best..! thanks in advance -

[gmx-users] Re: g_desort

Dear Jennifer: The line that worries me the most is: "I don't really want to try to figure out why gromacs-3.3.2 isn't working". First, I assume that you ran your mdrun under gmx-3.3.2 and I would think that you need to thoroughly understand why (and more importantly when) it broke. I may or

Re: [gmx-users] g_wham error

g_wham -ix PREPxvg.dat -it PREPtpr.dat The -ix option expects the pull positions. If you want to provide the pull forces to g_wham, use the -if option. Cheers, Jochen PREPxvg.dat and PREPtpr.dat are lists of the respective xvg and tpr files. They are both in the same order, although

[gmx-users] [help]How to produce .top file from Material Studio

Hi,everyone I have build a SiO2 structure in Material Studio, And I've set the xyz coordinates and force field parameters of the structure. Is there some tool or method to produce a .top file from MS. I do not want to write .top file line by line. Thanks. Di Cheng University of Science and Tech

Re: [gmx-users] Free Energy Calculation

Hi Anirban, You *could* use the configurations in your trajectory to (re)calculate average energies; by de-coupling your ligand this would get you the average free energy change per coupling strength change at the point where the ligand is fully bound. If you're interested in free energy of bi

[gmx-users] video: Introduction to molecular dynamics simulations

Dear All I would like to see the video that we can find in the website of Gromacs ( http://www.gromacs. org/Documentation/Terminology/Molecular_Dynamics_Simulations ) " Introduction to molecular dynamics simulations (slides,video) - (Bert de Groot, Phil Biggin) " but if I go on "video", it wil