[gmx-users] ForceField for SDPC(sphingomyelin)

Dear Gmx community I am new to memberane simulation. i want to simulate membrane, which consists DPPC and SDPC(Sphingomyelin). luckily, i got the force field and coordinates for DPPC (dppc.itp,dppc.pdb) from Doctor Peter Tieleman'websites.however,i cannot find the force field and coordinates for

Re: [gmx-users] Questions about water in Gromacs

Sorry to ask the obvoius, but did you try to perturbe the ordered structure of the water with some position restaints MD? Energy minimization? I might have misunderstood, but the ordering you describe ("the water core seems to be distributed evenly in the system") suggests that your system has b

RE: [gmx-users] This may be it, but what to do?

Marc, > 1. Generated a two molecule complex and saved as .pdb > 2. Parsed the file out to retain relative coordinates > of each molecule in separate .pdb files > 3. Run both resulting molecules through PRODRG server > to generate .gro files for GMX processing. FYI, you can use the editconf scrip

RE: [gmx-users] Questions about water in Gromacs

Justin, Have you simulated each of the components on their own, i.e. pure octane or water? That should help to start to pin down what the issue is, just take it one part at a time. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Ph

[gmx-users] Questions about water in Gromacs

Dear gmx-users:   I am now studying a reverse micelle system using Gromacs. The system is like this: Isooctane outside, AOT reverse micelle in the center and water core inside the reverse micelle. I didn't use standard Gromacs force field, instead I am using a force field transferred from CHARMM fo

[gmx-users] Solvating with glycerol

Hello, I have a small peptide that I'd like to solvate with glycerol (instead of water). I couldn't find a .gro and .itp file for glycerol in the top directory. I was wondering if anyone has such files and would be willing to share them? In looking at the other solvent .gro files (i.e. spc

RE: [gmx-users] g_hbond

On Wed, 2006-08-23 at 07:38 -0500, Moore, Jonathan (J) wrote: > Erik, > > Thanks for the explanations! I'm glad to see that the two things that were > causing me the main problems aren't bugs. > > If the reverse ordering in -hbm and -hbn output isn't a bug, then the > documentation certainly nee

Re: [gmx-users] SWM4-DP (Roux group polarizable water model) .itp file needed

Steven Kirk wrote: Hello, Does anyone on the list have a .itp file for the recent Roux group SWM4-DP polarizable water molecule model? DvS mentioned a couple of months back that recent polarizable water molecule models from this group, and also models from the van Gunsteren group [presumably

Re: 回复： Re: [gmx-users] Pobability o f conformational distributions!

xi zhao wrote: Dear sir: I can not konw how to use g_sham combining with PCA? can you give me a example? Thank you very much! you compute projections on e.g. the first three vectors (using g_anaeig) and feed those to g_sham. DO also run g_sham -h */David van der Spoel <[EMAIL PROTECTED]>

Re: [gmx-users] Measuring dihedral energy of various selections

Thanks a lot! Sometimes it can be sooo easy ciao Jan Neumann >> may I ask how do you get the potential energies from a >> simulation? Is it possible to get continuous energy-time >> graph for a system? >> > > Use the script g_energy on the .edr file from the simulation. > > Catch ya, >

回复： Re: [gmx-users] Pobability of con formational distributions!

Dear sir: I can not konw how to use g_sham  combining with PCA? can you give me a example? Thank you very much! David van der Spoel <[EMAIL PROTECTED]> 写道： xi zhao wrote:> Dear sirs:> How to calculate the probability of conformational distributions in > gromacs by PCA method? I often meet it, but

RE: [gmx-users] g_hbond

Erik, Thanks for the explanations! I'm glad to see that the two things that were causing me the main problems aren't bugs. If the reverse ordering in -hbm and -hbn output isn't a bug, then the documentation certainly needs to be updated. The online and paper manuals say that the -hbm output "O

Re: [gmx-users] protein in bilayer

Dňa St 23. August 2006 13:42 mahbubeh zarrabi napísal: > dear itamar > where is adress make-hole site? > thanks 3rd record on following page http://www.gromacs.org/contributed_by_users/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,5/ ___ gm

Re: [gmx-users] theory of MD

Look at these books: Allen, Tildesley. Computer simulation of liquids Frenkel, Smit. Understanding molecular simulation Leach A.R. Molecular modelling. Principles and applications Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil [EMAIL PROTECTED] wrote:

Re: [gmx-users] protein in bilayer

dear itamar where is adress make-hole site? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] protein in bilayer

this might help as well. http://www.dddc.ac.cn/embo04/practicals/9_16.htm#membraneproteinsinsertion Original-Nachricht Datum: Wed, 23 Aug 2006 14:31:35 +0300 Von: Itamar Kass <[EMAIL PROTECTED]> An: Discussion list for GROMACS users Betreff: Re: [gmx-users] protein in bilayer

Re: [gmx-users] g_hbond

Ok. I'm on it. A few things I can see right away, other things need a closer look. See comments below On Tue, 2006-08-22 at 16:02 -0500, Moore, Jonathan (J) wrote: > I'm still having problems with g_hbond. I've submitted a bugzilla report. > > - The hbond existence matrix in the -hbm output does

Re: [gmx-users] protein in bilayer

There is a nice rewriting of GROMACS, make_hole, at the site. This comes with good help file. Itamar. mahbubeh zarrabi wrote: Dear freinds I want to insert protein (K channel) in bilayer lipid.whould you please help me? best regard __ Do You Yah

[gmx-users] protein in bilayer

Dear freinds I want to insert protein (K channel) in bilayer lipid.whould you please help me? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com __

Re: [gmx-users] g_order

priyanka srivastava wrote: Hie All, While using the tool g_order I am getting NAN (not a number), as is pasted below: Atom 4 Tensor: x=-0.229462 , y=-0.180263, z=0.409725 Atom 5 Tensor: x=nan , y=nan, z=nan Atom 6 Tensor: x=nan , y=nan, z=nan Atom 7 Tensor: x=-0.219508 , y=-0.176833, z=0.396342

[gmx-users] g_order

Hie All, While using the tool g_order I am getting NAN (not a number), as is pasted below: Atom 4 Tensor: x=-0.229462 , y=-0.180263, z=0.409725 Atom 5 Tensor: x=nan , y=nan, z=nan Atom 6 Tensor: x=nan , y=nan, z=nan Atom 7 Tensor: x=-0.219508 , y=-0.176833, z=0.396342 Has anybody ever encountere

Re: [gmx-users] theory of MD

[EMAIL PROTECTED] wrote: Dear all, My question is on the theory of MD. I actually could not find any material which describes in detail about the time integration algorithm. 1) I wanted to know why the time integration algorithm has to be used, I mean the practical benefits of it. I want the