[gmx-users] g_lie query

Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there

[gmx-users] no-pbc simulation in parallel

Hi all, I am experiencing a strange error while trying to perform a parallel run with pbc=no. Just a core.*** file (at the very beginning) is created and nothing is written into the logfile. The simulation just stops. I use mpirun -np 8 mdrun_407f -pd 2 2 2 . The same system runs correctly if

Re: [gmx-users] Charge grps and cut-off

Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout

Re: [gmx-users] g_lie query

Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with

Re: [gmx-users] Charge grps and cut-off

Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.

Re: [gmx-users] Charge grps and cut-off

If gromacs assumes the aminoacid residues as charge groups by default then I have many residues which have 12 atoms since I am using an all-atom force field-charmm27(counting H). Is there a way to define charge groups? On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: If gromacs assumes the aminoacid residues as charge groups by default then I have many residues which have 12 atoms since I am using an all-atom force field-charmm27(counting H). It doesn't matter how many atoms are in a residue, it matters how many atoms are assigned to

Re: [gmx-users] Charge grps and cut-off

A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31 1.008 ; qtot -3.16 478

Re: [gmx-users] Charge grps and cut-off

This is the arginine entry in the rtp file. It assigns 12 atoms to charge grp 3. [ ARG ] [ atoms ] N NH1 -0.47 0 HN H 0.310 CA CT1 0.070 HA HB 0.090 CB CT2 -0.18 1 HB1 HA

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31

Re: [gmx-users] Charge grps and cut-off

Hi, So if I use PME for coloumb interactions, then what are my options? Would you then suggest breaking up the 12-atom charge grp in the arginine residue into 2 charge groups? Would it be enough to make the changes in the .rtp or parameters in other files must be changed? POoja On Sat, Jul

[gmx-users] pull code example

Hi all, Could anybody please share some working system to look at the pull code in gromacs? I did not find any examples in the WWW, unfortunately. Vitaly -- Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Need For a Script

Hey,.. Thank you for the script. I will keep in mind what you said next time. Samrat Pal From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a

[gmx-users] g_rmsf

Hi, I am running an npt simulation for a protein in water. For more than 50% of the residues the backbone atoms have been restrained by applying posrestraints. I ran g_rmsf to check if the pos-restraints were working well. When I do this selecting 'backbone' from the groups menu, my rmsf file

[gmx-users] (no subject)

Hi, I am studying polyglutamine regarding to my Ph.D work. Now my sequence is NH3+ -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-COO-. I would like to cap the N and C terminal with the protecting groups CH3CO and NHCH3 instead of NH3+ and COO- respectively (i.e. CH3CONH-Q-Q-Q-Q-Q-CONHCH3). I am using GROMACS

Re: [gmx-users] g_rmsf

Hi Pooja, Try to get a grip on the file types and what they contain. A .cpt file is a checkpoint file containing a single configuration. Not much fluctuation to expect there. This sort of analysis only makes sense for a trajectory, or at least an ensemble of structures. Try the .xtc or the .trr

[gmx-users] g_sas for martini coarse-grained particles

Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC lipid bilayer . I was going to use g_sas for that. But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. But, since the particles in the martini lipids are

[gmx-users] pull code example

I'd send a list of links except that the other end of a google search for gromacs pull code example has all of what you will need to broaden your general pull code understanding. The mailing list has an absolutely massive number of posts on this too. Chris. Hi all, Could anybody please

[gmx-users] gromacs-localp-3.0.2 installation problem

     Hi all, Hi all   I tried to install gromacs-localp-3.0.2 on Fedora 11. First, I successfully run ./configure:   …….. …….. config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating