Re: [gmx-users] regarding the free energy calculation of justin tutorial...

2012-12-01 Thread Justin Lemkul
On 12/1/12 1:18 AM, rama david wrote: Hi gromacs friends, I am doing the gromacs tutorial of Justin, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html When I wrote the command g_bar -f md*.xvg -o -oi -oh I stuck with

[gmx-users] About Packing of Lipids

2012-12-01 Thread vidhya sankar
Dear Justin , Thank you For your reply   I am following your   Protein lipids Tutorial  . I have Reached APL 61.14 A^2   Then I did Em And NVT equilibration  . As stated in your Tutorial . But After  NVT Equilibration    When I visualize My .gro File in VMD  I have Observed

Re: [gmx-users] About Packing of Lipids

2012-12-01 Thread Justin Lemkul
On 12/1/12 8:17 AM, vidhya sankar wrote: Dear Justin , Thank you For your reply I am following your Protein lipids Tutorial . I have Reached APL 61.14 A^2 Then I did Em And NVT equilibration . As stated in your Tutorial . But After NVT Equilibration When I visualize

[gmx-users] Question about dihedral angle notation

2012-12-01 Thread Andrew DeYoung
Hi, I am looking at the file ffbonded.itp located in the oplsaa.ff directory (usually located in /usr/local/gromacs/share/gromacs/top/oplsaa.ff). I see the following entry in the [ dihedraltypes ] section: C3 CT OH HO 3 0.41840 1.25520 0.0 -1.67360 0.0

[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, dihedral types with all GROMOS FFs

2012-12-01 Thread Payman Pirzadeh
Hello, I am trying to generate a topology file for my protein which has three disulfide bonds using ffG53a5. I realized in the topology file that the force field parameters for bonds, angle and dihedrals of my S-S bonds are missing. I found the following thread about this issue:

[gmx-users] Dimer jumping during simulation

2012-12-01 Thread Kavyashree M
Dear users, I have simulated a protein dimer using OPLS-AA in 4.5.3 version. Analysing simulation showed that one of the monomer is out side the box. I tried trjconv pbc -nojump and trjconv -pbc mol still some fraction of a time one of them goes out. Can anyone suggest some solution to this. I

Re: [gmx-users] Protein at given pH

2012-12-01 Thread Alexey Shvetsov
Justin Lemkul писал 07-11-2012 16:20: On 11/7/12 7:10 AM, Steven Neumann wrote: On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I

[gmx-users] Re: Dimer jumping during simulation

2012-12-01 Thread Kavyashree M
Dear users, I used -center along with -pbc mol selecting protein for both options Its fine now both monomers are in the box. Thanks kavya On Sun, Dec 2, 2012 at 1:47 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I have simulated a protein dimer using OPLS-AA in 4.5.3 version.

[gmx-users] help

2012-12-01 Thread 申昊
Hi everyone， I am a new one on using gromacs. Now I have some problems. [1] I want using g_analyze to calculate the self-ACF with the dist.xvg resulted from g_dist, the file nameddist.xvg consists two lists of time(ns) and distance(nm), respectively. (a)why the result shows a