[gmx-users] problem in applying position restrain on protein

Dear all, I am encountering problem in applying position restrain on my protein which is with lipid bilayer . Actually I want to do simulation of system protein-lipid bilayer to pack lipid around the protein for this I want to keep my protein constant and lipid should move around this .I am doing

[gmx-users] ffgmx:diffusion of oxygen

Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for mostl

Re: [gmx-users] ffgmx:diffusion of oxygen

Sunil Thapa wrote: Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such

[gmx-users] Re: Questions

Hi Lin, I bounce this mail to the gromacs user list as the issues are well off to be archived. > I have two stupid questions here. Well, that's up to us to decide ;) > 1. I want to get the proper structure of lysozyme. > > From your tutorials, 1LW9.pdb file is used. Potassium (K), chloride (CL)

[gmx-users] different result for entropy with normal mode analysis and schlitter-approximation

Dear Gromacs Users, I'm trying to calculate entropies from a md trajectory using g_anaeig. There are two ways to go (question at bottom ;-): 1. NMA and quasi-harmonic approximation: Use a bunch of snapshots (maybe 5-20), minimize each of them to very low maximum forces, calculate the hessian matri

Re: [gmx-users] problem in applying position restrain on protein

nitu sharma wrote: Dear all, I am encountering problem in applying position restrain on my protein which is with lipid bilayer . Actually I want to do simulation of system protein-lipid bilayer to pack lipid around the protein for this I want to keep my protein constant and lipid should mo

Re: [gmx-users] different result for entropy with normal mode analysis and schlitter-approximation

Hi Oliver, I think the eigenvalues in NMA are not the same (there used to be a factor of 2PI and the mass weighting). Maybe you can try my script from the user contributions and see if you get something more reasonable (use to flag -n to indicate that your eigenvalues are from NMA). Ran. oliver.

RE: [gmx-users] transport properties

Once you have correlation results then xmgrace software can do the integration. Regards From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of oguz gurbulak Sent: Tuesday, April 28, 2009 10:25 AM To: gmx-users@gromacs.org Subject: [gmx-users] transport p

RE: [gmx-users] transport properties

Dear K. Chae,   Thank you very much for your answer. I computed velocity auto-correlation (VAC) functions , but how can I integrate velocity auto-correlation (VAC) functions to get Diffusion coefficient using xmgrace software ? I have just used xmgrace to plot md result for analysis. And I have

[gmx-users] Thermodynamic integration with Martini force field

Dear Martini and GROMACS users, I am trying to perform thermodynamic integration on cg simulations using the Martini FF and GROMACS version 3.3.1 with double precision on a system containing a protein, lipids, water and Cl- ions. In the first test runs I tried to change the Martini atom type Qd

Re: [gmx-users] forcefield for free (neutral) amino acids

Dear chun feng, I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino acids

[gmx-users] Full implementation of CHARMM and AMBER in GROMACS?

Hello, I was jut curious, are there any plans to fully implement any other FF in gromacs. Particulary Im interested in CHARMM and AMBER. By full implementation of CHARMM I mean not simply taking the numbers from the CHARMM text file but calculating CHARMM-specific issues, like Urey-Bradley interac

[gmx-users] Error by pdb2gmx

Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the

Re: [gmx-users] Error by pdb2gmx

Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2

RE: [gmx-users] ffgmx:diffusion of oxygen

The issue is you don't have enough statistics to get a meaningful result. Three ways you can get more, more particles, more time, or multiply runs. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Roya

Re: [gmx-users] Error by pdb2gmx

Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably le

RE: [gmx-users] Error by pdb2gmx

If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.mo

Re: [gmx-users] Error by pdb2gmx

Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Th

Re: [gmx-users] Error by pdb2gmx

Yanmei Song wrote: Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not c

RE: [gmx-users] Error by pdb2gmx

That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical S

Re: [gmx-users] Full implementation of CHARMM and AMBER in GROMACS?

Hi, in the 4.0.4 version CHARMM is supported with most CHARMM specific energy terms (U-B, dihedrals,...). You can find more about it at http://www.dbb.su.se/User:Bjelkmar/Ffcharmm. The only missing thing in 4.0.4 is CMAP which is added to the latest development/CVS version. As far as I know Amber

[gmx-users] 10-4 Wall Potential.

Just wanting to confirm: The potential function for the 10-4 wall in GROMACS is of the form: VLJ = c12*density*pi/(5*r^10) - c6*density*pi/(2*r^4) It is NOT the same as the 10-4-3 function which is also sometimes used to model surface-fluid interactions? Thanks, Travis T. _

Re: [gmx-users] forcefield for free (neutral) amino acids

FyD wrote: Dear chun feng, I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino

[gmx-users] RE: transport properties

Please read about obtaining diffusion constant from VAC in the gromacs wiki. I wrote an individual article on that topic. Best, Vitaly Subject: RE: [gmx-users] transport properties > To: Discussion list for GROMACS users > Message-ID: <569363.99887...@web36304.mail.mud.yahoo.com> >