[gmx-users] membrane protein simulation

Title: membrane protein simulation Hi gmx-users I am trying to set up an ED experiment with the low resolution structure of a membrane protein in the hope of generating NMR-like structures. >From what I have read until now, I know that I should either restrain the transmembrane domain of th

[gmx-users] Basic question.

Hello Gmx-Users, I was trying to look at the data obtained from energy terms in few simulations using gromacs. After the initial 50/100ps equilibriation, the potential and total energy terms for the entire simulation is almost a constant. Is it so for all the simulations (if there is no much change

[gmx-users] How to simulate the system with 100 chains?

Hi, all,   I want to simulate a unit cell of a protein under pbc. The whole system consists of about 100 chains. In original .pdb file, some chain IDs are identical, for example, 'A' is used for different chains. When I used that file without revision, gmx showed error like that: Chain iden

Re: [gmx-users] water-vacuum-water simulation

luisa pugliese wrote: thank you very much for the message. However I don't understand how can I tell the program where in the box I want water to stay and where is vacuum. Can you please explain me in a more explicit way how to set up the system. Then, once I have set up the box with water on t

Re: [gmx-users] water-vacuum-water simulation

thank you very much for the message. However I don't understand how can I tell the program where in the box I want water to stay and where is vacuum. Can you please explain me in a more explicit way how to set up the system. Then, once I have set up the box with water on the outer part and vacuu

[gmx-users] Re: gromacs tutorial

Hi Michal, I think Mark has explained this well enough on the gromacs user list. But, since a tutorial is intended to learn something, I'll try to be more elaborate and give some additional suggestions and exercises. First of all, in the tutorial you're encouraged to look at the files (.pdb, .gr

Re: [gmx-users] changing form of nonbonded force fields

Mark Abraham wrote: Andre Ghizoni wrote: Dear gromacs users, I would like to know how and if it is possible to change the form of the lennard jones potential in gromacs. What I want to do is shift the LJ function some R radius to the right for one species, i.e. f(r-R). In effect my potenti

Re: [gmx-users] do the non-bong ennergy influence the opt imization?

zzhwise1 wrote: > hi all > as i use the l-bfgs to optimize my system ,which composed of two > monolayers that each contain 36 CH3(CH2)14COOH molecules ,when the > distance bettwen the two monolayes is 1.5nm,the minimization go > smoothly,but when decrease to 1.2nm,the monilayers turn over(A

Re: [gmx-users] water-vacuum-water simulation

luisa pugliese wrote: Dear all, I would like to perform a molecular dinamics simulation of a GPCR in a water-vacuum-water box system. Anybody knows if it is possible to do it with GROMACS and what should I do? Thank you to all Luisa = Luisa Pugliese, Ph.D. [EMAIL P