Re: [gmx-users] a residue move in extremely large scale in MD

Dear Catch ya,   I have watched the trajectory of the simulation. Besdies, I got the PDb file for the whole 10 ns MD every 500 ps. Then I compared all the PDB files generated, and it confirms that 1 specific residues moves in an extremely large space.   Can you give me an explaination on it?   C

Re: [gmx-users] Simulated annealing in implicit solvent

On 8/7/12 8:10 PM, Ольга Кононова wrote: Hello, I got a problem, trying to make preparation (in particular, heating from 0 to 300 K) of my system in implicit solvent (GBSA OBC model). For gradual heating I use simulated annealing (see mdp below) and sd integrator, which allows me do not use th

[gmx-users] Simulated annealing in implicit solvent

Hello, I got a problem, trying to make preparation (in particular, heating from 0 to 300 K) of my system in implicit solvent (GBSA OBC model). For gradual heating I use simulated annealing (see mdp below) and sd integrator, which allows me do not use thermostat. I also set up gen_vel = yes and

Re: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

On 8/08/2012 3:17 AM, rama david wrote: Hi Gromacs Friends, I am trying to install gromacs 4.5.4 in parallel operating system fedora 17 I am using dell T 3500 precision , 6C. I downloaded openmppi-1.6 Command line to install ./configure --prefix=/usr/local make all install For fftw 3.3.

RE: [gmx-users] a residue move in extremely large scale in MD

What information has "told you" that you have large scale movement? Where did that information come from, how was it generated? Have you watch the trajectory of this simulation to see how the residue actually moves? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharma

Re: [gmx-users] Hydroxyapatite MD odd behavior

Thank you Justing... We are working on your observations... We are sure that we will get back on this issue as soon as we figure out what we have done wrong... Best, On Mon, 06 Aug 2012 15:29:04 -0400, Justin Lemkul wrote > On 8/6/12 3:13 PM, Ramon Garduno wrote: > > On Mon, 06 Aug 2012 13:52:4

Re: [gmx-users] a residue move in extremely large scale in MD

Dear Marck,   Will you please give me some suggestions on how to decide whether the probelm is from periodic boundary conditions?   Cheers,   Acoot - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Monday, 6 August 2012 10:31 PM Subject: Re: [gmx-

Re: [gmx-users] About Shake and Lincs Algorithm

On 8/7/12 9:17 AM, vidhya sankar wrote: Dear Justin , Thank you for your Previous useful reply I Have used the Lincs Alogrithim for NPT Equlibration MD. But For Main MD I would like to use Shake Algorithim With Shake _tol = 0.1 with continuation = yes Is it Correct

[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

Hi Gromacs Friends, I am trying to install gromacs 4.5.4 in parallel operating system fedora 17 I am using dell T 3500 precision , 6C. I downloaded openmppi-1.6 Command line to install ./configure --prefix=/usr/local make all install For fftw 3.3.2 installation command line was . ./configu

[gmx-users] About Shake and Lincs Algorithm

Dear Justin ,    Thank you for your Previous useful  reply I Have used the Lincs Alogrithim for NPT Equlibration MD. But For Main MD I would like to use Shake Algorithim With Shake _tol = 0.1  with  continuation = yes Is it Correct to use two algorithm  for simulation of same

Re: [gmx-users] RE: tutorials for Coarse-Grained MD Simulation

On 8/7/12 6:51 AM, J Peterson wrote: Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and sourc

[gmx-users] RE: tutorials for Coarse-Grained MD Simulation

Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and source the files from rev_trans.tar.gz. How d

Re: [gmx-users] .top file

On 8/7/12 5:33 AM, Shima Arasteh wrote: Dear gmx users, I need to check a line of angle section in .top file. It is written: 2 1 3 5 What does the numbers show? the atom numbers of .pdb file? How can I check this line? The first three are atom numbers within the corre

Re: [gmx-users] Error in ligand coordinate file

On 8/7/12 5:08 AM, sai nitin wrote: Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Char

[gmx-users] .top file

 Dear gmx users, I need to check a line of angle section in .top file. It is written:     2 1 3 5 What does the numbers show? the atom numbers of .pdb file? How can I check this line? Thanks for your help. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] Error in ligand coordinate file

Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Charmm 27 FF second one is simulate ligand i

RE: [gmx-users] RE: tutorials for Coarse-Grained MD Simulation

Those tutorials show most important things (e.g. how to build topology for given system) in CG Martini ff using Gromacs. You do not have to merge anything. Commands are the same as for atomistic simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Jan _